Ferhat Alkan

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Jan GorodkinUniversity of CopenhagenVerified email at sund.ku.dk
Cesim ErtenComputer Science, University of ArizonaVerified email at cs.arizona.edu
William FallerNetherlands Cancer InstituteVerified email at nki.nl
Anne WenzelreNEW – Novo Nordisk Foundation Center for Stem Cell Medicine, University of CopenhagenVerified email at sund.ku.dk
Joana SilvaThe Netherlands Cancer Institute - NKIVerified email at nki.nl
Alexander JungeCo-Founder & CTO amass technologies. Formerly Head of Machine Learning Corti.ai. PhD BioinformaticsVerified email at amass.tech
Peter F StadlerProfessor of Bioinformatics, Univ. LeipzigVerified email at bioinf.uni-leipzig.de
Stefan Ernst SeemannUniversity of CopenhagenVerified email at rth.dk
Jakob Hull HavgaardUniversity of CopenhagenVerified email at rth.dk
Ivo HofackerUniversity of ViennaVerified email at tbi.univie.ac.at
John van der OostMicrobiology, Wageningen UniversityVerified email at wur.nl
Prarthana MohanrajuWageningen University & ResearchVerified email at wur.nl
Thomas SwartjesLaboratory of Microbiology, Wageningen University and ResearchVerified email at wur.nl
Raymond StaalsAssociate Professor, Wageningen UniversityVerified email at wur.nl
Xiaoyong PanShanghai Jiao Tong UniversityVerified email at sjtu.edu.cn
Lars Juhl JensenUniversity of CopenhagenVerified email at cpr.ku.dk
Christopher T. WorkmanTechnical University of Denmark, Department of Biotechnology and BiomedicineVerified email at dtu.dk
Christian GardePhD, Director of Bioinfomatics, Evaxion BiotechVerified email at evaxion-biotech.com
Christian von MeringProfessor of Computational Biology, University of Zurich and Swiss Institute of BioinformaticsVerified email at imls.uzh.ch
Alberto Santos-ZavaletaScientific Database CuratorVerified email at ccg.unam.mx

Ferhat Alkan

Postdoc in the Netherlands Cancer Institute

Verified email at nki.nl

Bioinformatics Computational Biology RNA Translation Ribosome


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CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters F Alkan, A Wenzel, C Anthon, JH Havgaard, J Gorodkin Genome biology 19, 1-13, 2018	151	2018
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks F Alkan, C Erten Bioinformatics 30 (4), 531-539, 2014	95	2014
RIsearch2: suffix array-based large-scale prediction of RNA–RNA interactions and siRNA off-targets F Alkan, A Wenzel, O Palasca, P Kerpedjiev, AF Rudebeck, PF Stadler, ... Nucleic acids research 45 (8), e60-e60, 2017	93	2017
Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Cas12a SCA Creutzburg, WY Wu, P Mohanraju, T Swartjes, F Alkan, J Gorodkin, ... Nucleic acids research 48 (6), 3228-3243, 2020	78	2020
RAIN: RNA–protein association and interaction networks A Junge, JC Refsgaard, C Garde, X Pan, A Santos, F Alkan, C Anthon, ... Database 2017, baw167, 2017	68	2017
CRISPR/Cas9 gRNA activity depends on free energy changes and on the target PAM context GI Corsi, K Qu, F Alkan, X Pan, Y Luo, J Gorodkin Nature Communications 13 (1), 3006, 2022	52	2022
Glucocorticoid receptor triggers a reversible drug-tolerant dormancy state with acquired therapeutic vulnerabilities in lung cancer S Prekovic, K Schuurman, I Mayayo-Peralta, AG Manjón, M Buijs, S Yavuz, ... Nature communications 12 (1), 4360, 2021	46	2021
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access AS Geissler, C Anthon, F Alkan, E González-Tortuero, LD Poulsen, ... Microbial Genomics 7 (2), 000524, 2021	18	2021
SiPAN: simultaneous prediction and alignment of protein–protein interaction networks F Alkan, C Erten Bioinformatics 31 (14), 2356-2363, 2015	17	2015
Identifying ribosome heterogeneity using ribosome profiling F Alkan, OG Wilkins, S Hernández-Pérez, S Ramalho, J Silva, J Ule, ... Nucleic Acids Research 50 (16), e95-e95, 2022	16	2022
Ribosome impairment regulates intestinal stem cell identity via ZAKɑ activation J Silva, F Alkan, S Ramalho, G Snieckute, S Prekovic, AK Garcia, ... Nature Communications 13 (1), 4492, 2022	15	2022
Joint profiling of miRNAs and mRNAs reveals miRNA mediated gene regulation in the Göttingen Minipig obesity model CMJ Mentzel, F Alkan, H Keinicke, MJ Jacobsen, J Gorodkin, M Fredholm, ... PLoS One 11 (11), e0167285, 2016	15	2016
RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications F Alkan, C Erten Bioinformatics 33 (4), 537-544, 2017	12	2017
Alternative cleavage and polyadenylation generates downstream uncapped RNA isoforms with translation potential Y Malka, F Alkan, S Ju, PR Körner, A Pataskar, E Shulman, ... Molecular Cell 82 (20), 3840-3855. e8, 2022	11	2022
Ribo-ODDR: Oligo design pipeline for experiment-specific rRNA depletion in ribo-seq F Alkan, J Silva, EP Barberà, WJ Faller Bioinformatics, 2021	9	2021
CRISPRi screen for enhancing heterologous α-amylase yield in Bacillus subtilis AS Geissler, AO Fehler, LD Poulsen, E González-Tortuero, ... Journal of Industrial Microbiology and Biotechnology 50 (1), kuac028, 2023	6	2023
Multimodal stimulation screens reveal unique and shared genes limiting T cell fitness CP Lin, PL Levy, A Alflen, G Apriamashvili, MA Ligtenberg, ... Cancer Cell 42 (4), 623-645. e10, 2024	3	2024
Structure of conflict graphs in constraint alignment problems and algorithms F Alkan, T Bıyıkoğlu, M Demange, C Erten Discrete Mathematics & Theoretical Computer Science 21 (4), 2019	1	2019
NAC-mediated ribosome localization regulates cell fate and metabolism in intestinal stem cells S Ramalho, F Alkan, S Prekovic, K Jastrzebski, E Pinto Barbera, ... bioRxiv, 2024.04. 29.591601, 2024		2024
RNA dicing regulates the expression of an oncogenic JAK1 isoform Y Malka, R van der Kammen, S Ju, F Alkan, C Lee, WJ Faller bioRxiv, 2024.02. 20.581186, 2024		2024

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