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

por Alkan, Ferhat, Silva, Joana, Pintó Barberà, Eric, Faller, William J.
Publicado 2021

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

por Alkan, Ferhat, Wenzel, Anne, Anthon, Christian, Havgaard, Jakob Hull, Gorodkin, Jan
Publicado 2018

CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context

por Corsi, Giulia I., Qu, Kunli, Alkan, Ferhat, Pan, Xiaoguang, Luo, Yonglun, Gorodkin, Jan
Publicado 2022

Joint Profiling of miRNAs and mRNAs Reveals miRNA Mediated Gene Regulation in the Göttingen Minipig Obesity Model

por Mentzel, Caroline M. Junker, Alkan, Ferhat, Keinicke, Helle, Jacobsen, Mette J., Gorodkin, Jan, Fredholm, Merete, Cirera, Susanna
Publicado 2016

Identifying ribosome heterogeneity using ribosome profiling

por Alkan, Ferhat, Wilkins, Oscar G, Hernández-Pérez, Santiago, Ramalho, Sofia, Silva, Joana, Ule, Jernej, Faller, William J
Publicado 2022

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

por Alkan, Ferhat, Wenzel, Anne, Palasca, Oana, Kerpedjiev, Peter, Rudebeck, Anders Frost, Stadler, Peter F., Hofacker, Ivo L., Gorodkin, Jan
Publicado 2017

Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a

por Creutzburg, Sjoerd C A, Wu, Wen Y, Mohanraju, Prarthana, Swartjes, Thomas, Alkan, Ferhat, Gorodkin, Jan, Staals, Raymond H J, van der Oost, John
Publicado 2020

RAIN: RNA–protein Association and Interaction Networks

por 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
Publicado 2017

BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access

por Geissler, Adrian Sven, Anthon, Christian, Alkan, Ferhat, González-Tortuero, Enrique, Poulsen, Line Dahl, Kallehauge, Thomas Beuchert, Breüner, Anne, Seemann, Stefan Ernst, Vinther, Jeppe, Gorodkin, Jan
Publicado 2021

Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential

por 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
Publicado 2022

CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis

por 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
Publicado 2022

Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation

por 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
Publicado 2022

Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer

por 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
Publicado 2021