Issue Date	Title	Author(s)
2015	GenOO : a programming framework for High Throughput Sequencing analysis	Maragkakis, Manolis; Alexiou, Panagiotis; Mourelatos, Zissimos
2015	The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing	Vourekas, Anastassios; Zheng, Ke; Fu, Qi; Maragkakis, Manolis; Alexiou, Panagiotis; Ma, Jing; Pillai, Ramesh S.; Mourelatos, Zissimos; Wang, P. Jeremy
2016	CLIPSeqTools — a novel bioinformatics CLIP-seq analysis suite	Maragkakis, Manolis; Alexiou, Panagiotis; Nakaya, Tadashi; Mourelatos, Zissimos
2016	Sequence-dependent but not sequence-specific piRNA adhesion traps mRNAs to the germ plasm	Vourekas, Anastassios; Alexiou, Panagiotis; Vrettos, Nicholas; Maragkakis, Manolis; Mourelatos, Zissimos
2017	Kc167, a widely used Drosophila cell line, contains an active primary piRNA pathway	Vrettos, Nicholas; Maragkakis, Manolis; Alexiou, Panagiotis; Mourelatos, Zissimos
2018	cCLIP-seq : retrieval of chimeric reads from HITS-CLIP (CLIP-seq) libraries	Alexiou, Panagiotis; Maragkakis, Manolis; Mourelatos, Zissimos; Vourekas, Anastassios
2018	Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis	Ibrahim, Fadia; Maragkakis, Manolis; Alexiou, Panagiotis; Mourelatos, Zissimos
2020	Multi-branch convolutional neural network for identification of small non-coding RNA genomic loci	Georgakilas, Georgios K.; Grioni, Andrea; Liakos, Konstantinos G.; Chalupova, Eliska; Plessas, Fotis C.; Alexiou, Panagiotis
2020	CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells	Štětková, Monika; Growková, Kateřina; Fojtík, Petr; Valčíková, Barbora; Palušová, Veronika; Verlande, Amandine; Jorda, Radek; Kryštof, Vladimír; Hejret, Václav; Alexiou, Panagiotis; Rotrekl, Vladimír; Uldrijan, Stjepan
2020	PENGUINN : precise exploration of nuclear G-quadruplexes using interpretable neural networks	Klimentova, Eva; Polacek, Jakub; Simecek, Petr; Alexiou, Panagiotis
2021	DIANA-miRGen v4 : indexing promoters and regulators for more than 1500 microRNAs	Perdikopanis, Nikos; Georgakilas, Georgios K.; Grigoriadis, Dimitris; Pierros, Vasilis; Kavakiotis, Ioannis; Alexiou, Panagiotis; Hatzigeorgiou, Artemis
2021	Modulation of Aub–TDRD interactions elucidates piRNA amplification and germplasm formation	Vrettos, Nicholas; Maragkakis, Manolis; Alexiou, Panagiotis; Sgourdou, Paraskevi; Ibrahim, Fadia; Palmieri, Daniel; Kirino, Yohei; Mourelatos, Zissimos
2021	Bioinformatics and machine learning approaches to understand the regulation of mobile genetic elements	Giassa, Ilektra-Chara; Alexiou, Panagiotis
2022	Fine-tuning transformers for genomic tasks	Martinek, Vlastimil; Cechak, David; Gresova, Katarina; Alexiou, Panagiotis; Simecek, Petr
2022	ENNGene : an Easy Neural Network model building tool for Genomics	Chalupová, Eliška; Vaculík, Ondřej; Poláček, Jakub; Jozefov, Filip; Majtner, Tomáš; Alexiou, Panagiotis
2022	miRBind : a deep learning method for miRNA binding classification	Klimentová, Eva; Hejret, Václav; Krčmář, Ján; Grešová, Katarína; Giassa, Ilektra-Chara; Alexiou, Panagiotis
2022	Small RNA targets : advances in prediction tools and high-throughput profiling	Grešová, Katarína; Alexiou, Panagiotis; Giassa, Ilektra-Chara
2023	SAP domain facilitates efficient loading of Ku onto DNA ends	Fulnecek, Jaroslav; Klimentova, Eva; Cairo, Albert; Valuchova Bukovcakova, Sona; Alexiou, Panagiotis; Prokop, Zbynek; Riha, Karel
2023	Beyond microRNAs : analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation	Hejret, Vaclav; Varadarajan, Nandan Mysore; Klimentova, Eva; Gresova, Katarina; Giassa, Ilektra-Chara; Vanacova, Stepanka; Alexiou, Panagiotis
2023	Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics	Martinek, Vlastimil; Martin, Jessica; Belair, Cedric; Payea, Matthew John; Malla, Sulochan; Alexiou, Panagiotis; Maragkakis, Manolis