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| Issue Date | Title | Author(s) |
| 2009 | Accurate microRNA target prediction correlates with protein repression levels | Maragkakis, Manolis; Alexiou, Panagiotis; Papadopoulos, Giorgio L.; Reczko, Martin; Dalamagas, Theodore; Giannopoulos, George; Goumas, George; Koukis, Evangelos; Kourtis, Kornilios; Simossis, Victor A.; Sethupathy, Praveen; Vergoulis, Thanasis; Koziris, Nectarios; Sellis, Timos; Tsanakas, Panagiotis; Hatzigeorgiou, Artemis G. |
| 2012 | Accurate microRNA target prediction using detailed binding site accessibility and machine learning on proteomics data | Reczko, Martin; Maragkakis, Manolis; Alexiou, Panagiotis; Papadopoulos, Giorgio L.; Hatzigeorgiou, Artemis G. |
| 2018 | cCLIP-seq : retrieval of chimeric reads from HITS-CLIP (CLIP-seq) libraries | Alexiou, Panagiotis; Maragkakis, Manolis; Mourelatos, Zissimos; Vourekas, Anastassios |
| 2016 | CLIPSeqTools — a novel bioinformatics CLIP-seq analysis suite | Maragkakis, Manolis; Alexiou, Panagiotis; Nakaya, Tadashi; Mourelatos, Zissimos |
| 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 |
| 2009 | DIANA-microT web server : elucidating microRNA functions through target prediction | Maragkakis, Manolis; Reczko, Martin; Simossis, Victor A.; Alexiou, Panagiotis; Papadopoulos, Giorgos L.; Dalamagas, Theodore; Giannopoulos, Giorgos; Goumas, G.; Koukis, Evangelos; Kourtis, Kornilios; Vergoulis, Thanasis; Koziris, Nectarios; Sellis, Timoleon; Tsanakas, Panayotis; Hatzigeorgiou, Artemis G. |
| 2011 | DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association | Maragkakis, Manolis; Vergoulis, Thanasis; Alexiou, Panagiotis; Reczko, Martin; Plomaritou, Kyriaki; Gousis, Mixail; Kourtis, Kornilios; Koziris, Nectarios; Dalamagas, Theodore; Hatzigeorgiou, Artemis G. |
| 2010 | The DIANA-mirExTra web server : from gene expression data to microRNA function | Alexiou, Panagiotis; Maragkakis, Manolis; Papadopoulos, Giorgio L.; Simmosis, Victor A.; Zhang, Lin; Hatzigeorgiou, Artemis G. |
| 2009 | DIANA-mirPath : integrating human and mouse microRNAs in pathways | Papadopoulos, Giorgos L.; Alexiou, Panagiotis; Maragkakis, Manolis; Reczko, Martin; Hatzigeorgiou, Artemis G. |
| 2012 | Functional microRNA targets in protein coding sequences | Reczko, Martin; Maragkakis, Manolis; Alexiou, Panagiotis; Grosse, Ivo; Hatzigeorgiou, Artemis G. |
| 2013 | FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns | Nakaya, Tadashi; Alexiou, Panagiotis; Maragkakis, Manolis; Chang, Alexandra; Mourelatos, Zissimos |
| 2015 | GenOO : a programming framework for High Throughput Sequencing analysis | Maragkakis, Manolis; Alexiou, Panagiotis; Mourelatos, Zissimos |
| 2013 | Identification of in vivo, conserved, TAF15 RNA binding sites reveals the impact of TAF15 on the neuronal transcriptome | Ibrahim, Fadia; Maragkakis, Manolis; Alexiou, Panagiotis; Maronski, Margaret A.; Dichter, Marc A.; Mourelatos, Zissimos |
| 2017 | Kc167, a widely used Drosophila cell line, contains an active primary piRNA pathway | Vrettos, Nicholas; Maragkakis, Manolis; Alexiou, Panagiotis; Mourelatos, Zissimos |
| 2009 | Lost in translation : an assessment and perspective for computational microRNA target identification | Alexiou, Panagiotis; Maragkakis, Manolis; Papadopoulos, Giorgos L.; Reczko, Martin; Hatzigeorgiou, Artemis G. |
| 2014 | A MicroRNA precursor surveillance system in quality control of MicroRNA synthesis | Liu, Xuhang; Zheng, Qi; Vrettos, Nicholas; Maragkakis, Manolis; Alexiou, Panagiotis; Gregory, Brian D.; Mourelatos, Zissimos |
| 2012 | Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis | Vourekas, Anastassios; Zheng, Qi; Alexiou, Panagiotis; Maragkakis, Manolis; Kirino, Yohei; Gregory, Brian D.; Mourelatos, Zissimos |
| 2013 | Mitochondrial protein BmPAPI modulates the length of mature piRNAs | Honda, Shozo; Kirino, Yoriko; Maragkakis, Manolis; Alexiou, Panagiotis; Ohtaki, Akashi; Murali, Ramachandran; Mourelatos, Zissimos; Kirino, Yohei |
| 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 |
| 2023 | The MOV10 RNA helicase is a dosage-dependent host restriction factor for LINE1 retrotransposition in mice | Guan, Yongjuan; Gao, Hongyan; Leu, N. Adrian; Vourekas, Anastassios; Alexiou, Panagiotis; Maragkakis, Manolis; Kang, Zhenlong; Mourelatos, Zissimos; Liang, Guanxiang; Wang, P. Jeremy |
