CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters
Alkan, Ferhat, Wenzel, Anne, Anthon, Christian, Havgaard, Jakob Hull, Gorodkin, Jan
Published in Genome Biology (26.10.2018)
Published in Genome Biology (26.10.2018)
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Journal Article
CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context
Corsi, Giulia I., Qu, Kunli, Alkan, Ferhat, Pan, Xiaoguang, Luo, Yonglun, Gorodkin, Jan
Published in Nature communications (30.05.2022)
Published in Nature communications (30.05.2022)
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Journal Article
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets
Alkan, Ferhat, Wenzel, Anne, Palasca, Oana, Kerpedjiev, Peter, Rudebeck, Anders Frost, Stadler, Peter F, Hofacker, Ivo L, Gorodkin, Jan
Published in Nucleic acids research (05.05.2017)
Published in Nucleic acids research (05.05.2017)
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Journal Article
Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer
Prekovic, Stefan, Schuurman, Karianne, Mayayo-Peralta, Isabel, Manjón, Anna G., Buijs, Mark, Yavuz, Selçuk, Wellenstein, Max D., Barrera, Alejandro, Monkhorst, Kim, Huber, Anne, Morris, Ben, Lieftink, Cor, Chalkiadakis, Theofilos, Alkan, Ferhat, Silva, Joana, Győrffy, Balázs, Hoekman, Liesbeth, van den Broek, Bram, Teunissen, Hans, Debets, Donna O., Severson, Tesa, Jonkers, Jos, Reddy, Timothy, de Visser, Karin E., Faller, William, Beijersbergen, Roderick, Altelaar, Maarten, de Wit, Elzo, Medema, Rene, Zwart, Wilbert
Published in Nature communications (16.07.2021)
Published in Nature communications (16.07.2021)
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Journal Article
Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation
Silva, Joana, Alkan, Ferhat, Ramalho, Sofia, Snieckute, Goda, Prekovic, Stefan, Garcia, Ana Krotenberg, Hernández-Pérez, Santiago, van der Kammen, Rob, Barnum, Danielle, Hoekman, Liesbeth, Altelaar, Maarten, Zwart, Wilbert, Suijkerbuijk, Saskia Jacoba Elisabeth, Bekker-Jensen, Simon, Faller, William James
Published in Nature communications (02.08.2022)
Published in Nature communications (02.08.2022)
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Journal Article
Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model
Mentzel, Caroline M Junker, Alkan, Ferhat, Keinicke, Helle, Jacobsen, Mette J, Gorodkin, Jan, Fredholm, Merete, Cirera, Susanna
Published in PloS one (01.11.2016)
Published in PloS one (01.11.2016)
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Journal Article
Ribo-ODDR: oligo design pipeline for experiment-specific rRNA depletion in Ribo-seq
Alkan, Ferhat, Silva, Joana, Pintó Barberà, Eric, Faller, William J.
Published in Bioinformatics (Oxford, England) (09.09.2021)
Published in Bioinformatics (Oxford, England) (09.09.2021)
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Journal Article
Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a
Creutzburg, Sjoerd C A, Wu, Wen Y, Mohanraju, Prarthana, Swartjes, Thomas, Alkan, Ferhat, Gorodkin, Jan, Staals, Raymond H J, van der Oost, John
Published in Nucleic acids research (06.04.2020)
Published in Nucleic acids research (06.04.2020)
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Journal Article
Identifying ribosome heterogeneity using ribosome profiling
Alkan, Ferhat, Wilkins, Oscar G, Hernández-Pérez, Santiago, Ramalho, Sofia, Silva, Joana, Ule, Jernej, Faller, William J
Published in Nucleic acids research (09.09.2022)
Published in Nucleic acids research (09.09.2022)
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Journal Article
Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential
Malka, Yuval, Alkan, Ferhat, Ju, Shinyeong, Körner, Pierre-Rene, Pataskar, Abhijeet, Shulman, Eldad, Loayza-Puch, Fabricio, Champagne, Julien, Wenzel, Casper, Faller, William James, Elkon, Ran, Lee, Cheolju, Agami, Reuven
Published in Molecular cell (20.10.2022)
Published in Molecular cell (20.10.2022)
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Journal Article
P-stalk ribosomes act as master regulators of cytokine-mediated processes
Dopler, Anna, Alkan, Ferhat, Malka, Yuval, van der Kammen, Rob, Hoefakker, Kelly, Taranto, Daniel, Kocabay, Naz, Mimpen, Iris, Ramirez, Christel, Malzer, Elke, Isaeva, Olga I, Kerkhoff, Mandy, Gangaev, Anastasia, Silva, Joana, Ramalho, Sofia, Hoekman, Liesbeth, Altelaar, Maarten, Beijersbergen, Roderick, Akkari, Leila, Yewdell, Jonathan Wilson, Kvistborg, Pia, Faller, William James
Published in Cell (14.10.2024)
Published in Cell (14.10.2024)
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Journal Article
EXTH-72. TARGETED INHIBITION OF THREE MAJOR PROLIFERATION PATHWAYS IN GLIOBLASTOMA INDUCES SENESCENCE THROUGH A MITOCHONDRIA-DEPENDENT MECHANISM
Baltira, Chrysiida, Mayayo-Peralta, Isabel, Guillen-Navarro, Miriam, Alkan, Ferhat, Thijssen, Bram, Pello, Kimberley, Fedorushkova, Daria, Their, Anna, Silva, Joana, Jochems, Fleur, Bleijerveld, Onno, Janssen, Hans, Faller, William, Bernards, Rene, de Gooijer, Mark, van Tellingen, Olaf
Published in Neuro-oncology (Charlottesville, Va.) (10.11.2023)
Published in Neuro-oncology (Charlottesville, Va.) (10.11.2023)
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Journal Article
CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis
Geissler, Adrian Sven, Fehler, Annaleigh Ohrt, Poulsen, Line Dahl, González-Tortuero, Enrique, Kallehauge, Thomas Beuchert, Alkan, Ferhat, Anthon, Christian, Seemann, Stefan Ernst, Rasmussen, Michael Dolberg, Breüner, Anne, Hjort, Carsten, Vinther, Jeppe, Gorodkin, Jan
Published in Journal of industrial microbiology & biotechnology (17.02.2023)
Published in Journal of industrial microbiology & biotechnology (17.02.2023)
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Journal Article
Structure of conflict graphs in constrained alignment problems and algorithms
Alkan, Ferhat, Biyikoglu, Turker, Demange, Marc, Erten, Cesim
Published in Discrete Mathematics and Theoretical Computer Science (01.08.2019)
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Published in Discrete Mathematics and Theoretical Computer Science (01.08.2019)
Journal Article
Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness
Lin, Chun-Pu, Levy, Pierre L., Alflen, Astrid, Apriamashvili, Georgi, Ligtenberg, Maarten A., Vredevoogd, David W., Bleijerveld, Onno B., Alkan, Ferhat, Malka, Yuval, Hoekman, Liesbeth, Markovits, Ettai, George, Austin, Traets, Joleen J.H., Krijgsman, Oscar, van Vliet, Alex, Poźniak, Joanna, Pulido-Vicuña, Carlos Ariel, de Bruijn, Beaunelle, van Hal-van Veen, Susan E., Boshuizen, Julia, van der Helm, Pim W., Díaz-Gómez, Judit, Warda, Hamdy, Behrens, Leonie M., Mardesic, Paula, Dehni, Bilal, Visser, Nils L., Marine, Jean-Christophe, Markel, Gal, Faller, William J., Altelaar, Maarten, Agami, Reuven, Besser, Michal J., Peeper, Daniel S.
Published in Cancer cell (08.04.2024)
Published in Cancer cell (08.04.2024)
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Journal Article
RAIN: RNA–protein Association and Interaction Networks
Junge, Alexander, Refsgaard, Jan C., Garde, Christian, Pan, Xiaoyong, Santos, Alberto, Alkan, Ferhat, Anthon, Christian, von Mering, Christian, Workman, Christopher T., Jensen, Lars Juhl, Gorodkin, Jan
Published in Database : the journal of biological databases and curation (01.01.2017)
Published in Database : the journal of biological databases and curation (01.01.2017)
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Journal Article
Structure of conflict graphs in constraint alignment problems and algorithms
Ferhat Alkan, Türker Bıyıkoğlu, Marc Demange, Cesim Erten
Published in Discrete mathematics and theoretical computer science (01.09.2019)
Published in Discrete mathematics and theoretical computer science (01.09.2019)
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