Dr. Ferhat Alkan

P-stalk ribosomes act as master regulators of cytokine-mediated processes

Dopler, A., ..., Alkan, F., et al.

Cell

Groundbreaking discovery identifying alert-state ribosomes defined by P-stalk presence, showing their formation in response to cytokines linked to tumor immunity. This work reveals a novel mechanism of translational control in cancer immunology.

Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data

Alkan, F., Kyei-Baffour, E.S., Bak, J., Silva, J., Faller, W.J.

NAR Genomics and Bioinformatics

Introduced dricARF (differential ribosome collisions by Analysis of rRNA Fragments), a novel computational approach enabling relative quantification of ribosome collisions between samples, revealing translational stress mechanisms.

Loss of ribosomal protein uL14 enables tumor escape from T cell immunosurveillance

Alkan, F., et al.

NAR Cancer

Discovered a critical mechanism by which loss of ribosomal protein uL14 enables tumors to evade T cell-mediated immune responses. This work reveals how alterations in ribosome composition can contribute to tumor immune escape, providing insights into cancer immunotherapy resistance and potential therapeutic targets.

High-throughput approaches for the identification of ribosome heterogeneity

Alkan, F., Kyei-Baffour, E.S., Lin, Q.C., Faller, W.J.

Philosophical Transactions of the Royal Society B

Comprehensive review of cutting-edge high-throughput techniques for identifying ribosomal heterogeneity, covering methodologies for probing both rRNA and protein components through next-generation sequencing, computational analyses, and mass spectrometry.

Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq

Alkan, F., Silva, J., Pintó, S.V., Faller, W.J.

Bioinformatics

Developed an intelligent oligo design pipeline with user-friendly interface that dramatically improves rRNA depletion efficiency in ribosome profiling experiments. Ribo-ODDR-designed oligos outperform commercial kits, addressing the critical challenge that rRNA fragments comprise >90% of sequencing reads if not properly depleted.

🔗 Open-source tool available at github.com/fallerlab/Ribo-ODDR

CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters

Alkan, F., Wenzel, A., Anthon, C., Havgaard, J.H., Gorodkin, J.

Genome Biology

Pioneered approximate binding energy models for Cas9-gRNA-DNA complexes by systematically combining energy parameters for RNA-RNA, DNA-DNA, and RNA-DNA duplexes. Introduced two breakthrough methods: CRISPRoff for assigning confidence scores to predicted off-targets, and CRISPRspec for measuring gRNA specificity.

RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets

Alkan, F., Wenzel, A., Palasca, O., Kerpedjiev, P., Rudebeck, A.F., Stadler, P.F., Hofacker, I.L., Gorodkin, J.

Nucleic Acids Research

Revolutionary suffix array-based algorithm achieving 1-2 orders of magnitude faster performance than existing methods (IntaRNA, RNAplex) for large-scale RNA-RNA interaction prediction. Enables genome-wide screens previously computationally prohibitive, with applications in siRNA off-target identification and regulatory RNA discovery.

RAIN: RNA–protein Association and Interaction Networks

Alkan, F., et al.

Database (Oxford)

Created comprehensive database integrating ncRNA-ncRNA, ncRNA-mRNA, and ncRNA-protein interactions with large-scale protein association networks from STRING database. RAIN combines curated examples, experimental data, computational predictions, and literature mining across four model organisms.

🔗 Database accessible at rth.dk/resources/rain/

BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks

Alkan, F., Erten, C.

Bioinformatics

Developed innovative heuristic method for global many-to-many alignment of protein-protein interaction networks by grouping functionally orthologous proteins. BEAMS decomposes the complex alignment problem into backbone extraction and merging subproblems, achieving superior performance with reasonable computational burden compared to state-of-the-art approaches.

Structure of conflict graphs in constraint alignment problems and algorithms

Alkan, F., Erten, C.

Discrete Mathematics & Theoretical Computer Science

Theoretical foundations for constrained graph alignment problems in biological network analysis, formulating the problem as maximum independent set in conflict graphs with applications to comparative genomics.