Ferhat Alkan
Title
Cited by
Cited by
Year
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
752014
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
512017
RAIN: RNA–protein Association and Interaction Networks
A Junge, JC Refsgaard, C Garde, X Pan, A Santos, F Alkan, C Anthon, ...
Database 2017, 2017
492017
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), 1-13, 2018
402018
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
152020
SiPAN: simultaneous prediction and alignment of protein–protein interaction networks
F Alkan, C Erten
Bioinformatics 31 (14), 2356-2363, 2015
132015
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
112016
RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications
F Alkan, C Erten
Bioinformatics 33 (4), 537-544, 2017
72017
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
2*2019
Ribo-ODDR: Oligo design pipeline for experiment-specific rRNA depletion in ribo-seq
F Alkan, J Silva, EP Barberà, WJ Faller
Bioinformatics, 2021
1*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
2021
A Study of Pig Chromosome X lncRNA Expression
S Djebali, O Palasca, C Anthon, T Derrien, O Madsen, M Thomas, ...
The Plant and Animal Genome XXIIV Conference (PAG), 2017
2017
Global many-to-many aligment of multiple protein-protein interaction networks
F Alkan
Kadir Has University [MSc Thesis], 2013
2013
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Articles 1–13