Publications by authors named "Ferhat Alkan"

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Loss of ribosomal protein uL14 enables tumor escape from T cell immunosurveillance.
Anna Dopler, Edwin S Kyei-Baffour, Mandy Kerkhoff, Ferhat Alkan, Yuval Malka

NAR Cancer· September 2025

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Is there any room for ChatGPT AI bot in speech-language pathology?
Namık Yücel Birol, Hilal Berber Çiftci, Ayşegül Yılmaz, Ayhan Çağlayan, Ferhat Alkan

Eur Arch Otorhinolaryngol· June 2025

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Correction: Is there any room for ChatGPT AI bot in speech-language pathology?
Namık Yücel Birol, Hilal Berber Çiftci, Ayşegül Yılmaz, Ayhan Çağlayan, Ferhat Alkan

Eur Arch Otorhinolaryngol· June 2025

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Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data.
Edwin Sakyi Kyei-Baffour, Jitske Bak, Joana Silva, William J Faller, Ferhat Alkan

NAR Genom Bioinform· June 2025

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High-throughput approaches for the identification of ribosome heterogeneity.
Edwin S Kyei-Baffour, Qi Chang Lin, Ferhat Alkan, William J Faller

Philos Trans R Soc Lond B Biol Sci· March 2025

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NAC regulates metabolism and cell fate in intestinal stem cells.
Sofia Ramalho, Ferhat Alkan, Stefan Prekovic, Katarzyna Jastrzebski, Eric Pintó Barberà

Sci Adv· January 2025

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P-stalk ribosomes act as master regulators of cytokine-mediated processes.
Anna Dopler, Ferhat Alkan, Yuval Malka, Rob van der Kammen, Kelly Hoefakker

Cell· November 2024

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Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness.
Chun-Pu Lin, Pierre L Levy, Astrid Alflen, Georgi Apriamashvili, Maarten A Ligtenberg, Ferhat Alkan

Cancer Cell· April 2024

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CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis.
Adrian Sven Geissler, Annaleigh Ohrt Fehler, Line Dahl Poulsen, Enrique González-Tortuero, Thomas Beuchert Kallehauge, Ferhat Alkan

J Ind Microbiol Biotechnol· February 2023

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Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential.
Yuval Malka, Ferhat Alkan, Shinyeong Ju, Pierre-Rene Körner, Abhijeet Pataskar

Mol Cell· October 2022

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Identifying ribosome heterogeneity using ribosome profiling.
Ferhat Alkan, Oscar G Wilkins, Santiago Hernández-Pérez, Sofia Ramalho, Joana Silva

Nucleic Acids Res· September 2022

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Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation.
Joana Silva, Ferhat Alkan, Sofia Ramalho, Goda Snieckute, Stefan Prekovic

Nat Commun· August 2022

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CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context.
Giulia I Corsi, Kunli Qu, Ferhat Alkan, Xiaoguang Pan, Yonglun Luo

Nat Commun· May 2022

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Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq.
Ferhat Alkan, Joana Silva, Eric Pintó Barberà, William J Faller

Bioinformatics· September 2021

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Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer.
Stefan Prekovic, Karianne Schuurman, Isabel Mayayo-Peralta, Anna G Manjón, Mark Buijs, Ferhat Alkan

Nat Commun· July 2021

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BSGatlas: a unified genome and transcriptome annotation atlas with enhanced information access.
Adrian Sven Geissler, Christian Anthon, Ferhat Alkan, Enrique González-Tortuero, Line Dahl Poulsen

Microb Genom· February 2021

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Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a.
Sjoerd C A Creutzburg, Wen Y Wu, Prarthana Mohanraju, Thomas Swartjes, Ferhat Alkan

Nucleic Acids Res· April 2020

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CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters.
Ferhat Alkan, Anne Wenzel, Christian Anthon, Jakob Hull Havgaard, Jan Gorodkin

Genome Biol· October 2018

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RAIN: RNA-protein Association and Interaction Networks.
Alexander Junge, Jan C Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan

Database (Oxford)· November 2017

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Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model.
Caroline M Junker Mentzel, Ferhat Alkan, Helle Keinicke, Mette J Jacobsen, Jan Gorodkin

PLoS One· July 2017

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RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck

Nucleic Acids Res· May 2017

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RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications.
Ferhat Alkan, Cesim Erten

Bioinformatics· February 2017

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SiPAN: simultaneous prediction and alignment of protein-protein interaction networks.
Ferhat Alkan, Cesim Erten

Bioinformatics· July 2015

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BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks.
Ferhat Alkan, Cesim Erten

Bioinformatics· February 2014

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