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Panagiotis Alexiou · SciRah

Researcher profile · Semantic Scholar

Panagiotis Alexiou

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Panagiotis Alexiou — researcher profile on SciRah

h-index: 23
Works: 68
Citations: 4,046

Most-cited papers

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support
Thanasis Vergoulis, I. Vlachos, Panagiotis Alexiou, George Georgakilas +6 more
2011Nucleic Acids Res.586 citations Open access
Semantic Scholar
Functional microRNA targets in protein coding sequences
M. Reczko, Manolis Maragkakis, Panagiotis Alexiou, I. Grosse +1 more
2012Bioinform.502 citations Open access
Semantic Scholar
DIANA-microT web server: elucidating microRNA functions through target prediction
Manolis Maragkakis, M. Reczko, V. Simossis, Panagiotis Alexiou +11 more
2009Nucleic Acids Res.388 citations Open access
Semantic Scholar
Lost in translation: an assessment and perspective for computational microRNA target identification
Panagiotis Alexiou, Manolis Maragkakis, Giorgos L. Papadopoulos, M. Reczko +1 more
2009Bioinform.355 citations Open access
Semantic Scholar
DIANA-mirPath: Integrating human and mouse microRNAs in pathways
Giorgos L. Papadopoulos, Panagiotis Alexiou, Manolis Maragkakis, M. Reczko +1 more
2009Bioinform.288 citations Open access
Semantic Scholar
Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis
Anastassios Vourekas, Qi Zheng, Panagiotis Alexiou, Manolis Maragkakis +3 more
2012Nature Structural &Molecular Biology252 citations Open access
Semantic Scholar
The RNA helicase MOV10L1 binds piRNA precursors to initiate piRNA processing
Anastassios Vourekas, Ke Zheng, Q. Fu, Manolis Maragkakis +5 more
2015Genes & Development161 citations Open access
Semantic Scholar
DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association
Manolis Maragkakis, Thanasis Vergoulis, Panagiotis Alexiou, M. Reczko +6 more
2011Nucleic Acids Res.149 citations Open access
Semantic Scholar
Genomic benchmarks: a collection of datasets for genomic sequence classification
Katarína Grešová, Vlastimil Martinek, David Čechák, P. Simecek +1 more
2022bioRxiv140 citations Open access
Semantic Scholar
miRGen 2.0: a database of microRNA genomic information and regulation
Panagiotis Alexiou, Thanasis Vergoulis, Martin Gleditzsch, George Prekas +5 more
2009Nucleic Acids Res.140 citations Open access
Semantic Scholar
Sequence-dependent but not sequence-specific piRNA adhesion traps mRNAs to the germ plasm
Anastassios Vourekas, Panagiotis Alexiou, Nicholas Vrettos, Manolis Maragkakis +1 more
2016Nature133 citations Open access
Semantic Scholar
FUS regulates genes coding for RNA-binding proteins in neurons by binding to their highly conserved introns.
T. Nakaya, Panagiotis Alexiou, Manolis Maragkakis, A. Chang +1 more
2013RNA: A publication of the RNA Society124 citations Open access
Semantic Scholar
A MicroRNA Precursor Surveillance System in Quality Control of MicroRNA Synthesis
Xuhang Liu, Qi Zheng, Nicholas Vrettos, Manolis Maragkakis +3 more
2014Molecules and Cells85 citations Open access
Semantic Scholar
The DIANA-mirExTra Web Server: From Gene Expression Data to MicroRNA Function
Panagiotis Alexiou, Manolis Maragkakis, G. Papadopoulos, Victor A. Simmosis +2 more
2010PLoS ONE84 citations Open access
Semantic Scholar
Mitochondrial protein BmPAPI modulates the length of mature piRNAs
Shozo Honda, Yoriko Kirino, Manolis Maragkakis, Panagiotis Alexiou +4 more
2013RNA: A publication of the RNA Society81 citations Open access
Semantic Scholar
Hormone-regulated expansins: Expression, localization, and cell wall biomechanics in Arabidopsis root growth
Marketa Samalova, Alesia Melnikava, K. Elsayad, A. Peaucelle +12 more
2023Plant Physiology59 citations Open access
Semantic Scholar
Ribothrypsis, a novel process of canonical mRNA decay, mediates ribosome-phased mRNA endonucleolysis
Fadia Ibrahim, Manolis Maragkakis, Panagiotis Alexiou, Z. Mourelatos
2018Nature Structural & Molecular Biology56 citations Open access
Semantic Scholar
In vivo profiling of hypoxic gene expression in gliomas using the hypoxia marker EF5 and laser-capture microdissection
D. Marotta, J. Karar, W. Jenkins, M. Kumanova +10 more
2011Cancer Research56 citations Open access
Semantic Scholar
Identification of in vivo, conserved, TAF15 RNA binding sites reveals the impact of TAF15 on the neuronal transcriptome
Fadia Ibrahim, Manolis Maragkakis, Panagiotis Alexiou, M. Maronski +2 more
2013Cell Reports51 citations Open access
Semantic Scholar
CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite
Manolis Maragkakis, Panagiotis Alexiou, T. Nakaya, Z. Mourelatos
2016RNA: A publication of the RNA Society44 citations Open access
Semantic Scholar
Accurate microRNA Target Prediction Using Detailed Binding Site Accessibility and Machine Learning on Proteomics Data
M. Reczko, Manolis Maragkakis, Panagiotis Alexiou, G. Papadopoulos +1 more
2011Front. Gene.43 citations Open access
Semantic Scholar
PENGUINN: Precise Exploration of Nuclear G-Quadruplexes Using Interpretable Neural Networks
E. Klimentova, Jakub Polácek, P. Simecek, Panagiotis Alexiou
2020bioRxiv32 citations Open access
Semantic Scholar
DIANA-miRGen v4: indexing promoters and regulators for more than 1500 microRNAs
Nikos Perdikopanis, G. Georgakilas, Dimitris Grigoriadis, Vasilis Pierros +3 more
2020Nucleic Acids Res.23 citations Open access
Semantic Scholar
CDK9 activity is critical for maintaining MDM4 overexpression in tumor cells
Monika Štětková, K. Growková, P. Fojtík, Barbora Valčíková +8 more
2020Cell Death and Disease23 citations Open access
Semantic Scholar
Kc167, a widely used Drosophila cell line, contains an active primary piRNA pathway
Nicholas Vrettos, Manolis Maragkakis, Panagiotis Alexiou, Z. Mourelatos
2017RNA: A publication of the RNA Society19 citations Open access
Semantic Scholar
Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation
V. Hejret, Nandan Mysore Varadarajan, E. Klimentova, Katarína Grešová +3 more
2023Scientific Reports18 citations Open access
Semantic Scholar
Multi-branch Convolutional Neural Network for Identification of Small Non-coding RNA genomic loci
G. Georgakilas, A. Grioni, Konstantinos G. Liakos, Eliška Chalupová +2 more
2020Scientific Reports16 citations Open access
Semantic Scholar
Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling
Katarína Grešová, Panagiotis Alexiou, Ilektra-Chara Giassa
2022Biology15 citations Open access
Semantic Scholar
miRBind: A Deep Learning Method for miRNA Binding Classification
E. Klimentova, V. Hejret, J. Krčmář, Katarína Grešová +2 more
2022Genes13 citations Open access
Semantic Scholar
Modulation of Aub–TDRD interactions elucidates piRNA amplification and germplasm formation
Nicholas Vrettos, Manolis Maragkakis, Panagiotis Alexiou, Paraskevi Sgourdou +4 more
2020Life Science Alliance13 citations Open access
Semantic Scholar
Agentomics: an agentic system that autonomously develops novel state-of-the-art solutions for biomedical machine learning tasks
Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Mark Galea +7 more
2026bioRxiv11 citations Open access
Semantic Scholar
miRBench: novel benchmark datasets for microRNA binding site prediction that mitigate against prevalent microRNA frequency class bias
S. Sammut, Katarína Grešová, Dimosthenis Tzimotoudis, Eva Maršálková +2 more
2025bioRxiv11 citations Open access
Semantic Scholar
The SAP domain of Ku facilitates its efficient loading onto DNA ends
Jaroslav Fulneček, E. Klimentova, Albert Cairó, Sona Valuchova Bukovcakova +3 more
2023Nucleic Acids Research11 citations Open access
Semantic Scholar
ENNGene: an Easy Neural Network model building tool for Genomics
Eliška Chalupová, Ondřej Vaculík, Jakub Polácek, Filip Jozefov +2 more
2021BMC Genomics8 citations Open access
Semantic Scholar
The MOV10 RNA helicase is a dosage-dependent host restriction factor for LINE1 retrotransposition in mice
Yong-Juan Guan, Hong-Yan Gao, N. Leu, Anastassios Vourekas +6 more
2022bioRxiv7 citations Open access
Semantic Scholar
Transfer Learning Allows Accurate RBP Target Site Prediction with Limited Sample Sizes
Ondřej Vaculík, Eliška Chalupová, Katarína Grešová, Tomáš Majtner +1 more
2023Biology6 citations Open access
Semantic Scholar
Fine-Tuning Transformers For Genomic Tasks
Vlastimil Martinek, David Čechák, Katarína Grešová, Panagiotis Alexiou +1 more
2022bioRxiv6 citations Open access
Semantic Scholar
Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements
Ilektra-Chara Giassa, Panagiotis Alexiou
2021Biology6 citations Open access
Semantic Scholar
Using Attribution Sequence Alignment to Interpret Deep Learning Models for miRNA Binding Site Prediction
Katarína Grešová, Ondřej Vaculík, Panagiotis Alexiou
2023Biology5 citations Open access
Semantic Scholar
Bottlenecks in advancing and applying multiomic data integration—common data resources as rate-limiting drivers—the high-impact use case of atherosclerotic cardiovascular disease
S. Bezzina Wettinger, Kanita Karaduzovic-Hadziabdic, Ritienne Attard, Rosienne Farrugia +19 more
2025Briefings Bioinform.4 citations Open access
Semantic Scholar
Agentomics-ML: Autonomous Machine Learning Experimentation Agent for Genomic and Transcriptomic Data
Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Aitor Alberdi Escudero +5 more
2025arXiv.org4 citations
Semantic Scholar
Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics.
Vlastimil Martinek, Jessica Martin, Cédric Belair, Matthew J. Payea +3 more
2024NAR Genomics and Bioinformatics4 citations Open access
Semantic Scholar
Identification of genes used by Escherichia coli to mitigate climatic stress conditions
S. Roufou, Sholeem Griffin, L. Katsini, M. Polanska +3 more
2024Gene Reports3 citations Open access
Semantic Scholar
RBP-Tar – a searchable database for experimental RBP binding sites
Katarína Grešová, T. Racek, Vlastimil Martinek, David Čechák +2 more
2023F1000Research3 citations Open access
Semantic Scholar
Deep learning and direct sequencing of labeled RNA captures transcriptome dynamics
Vlastimil Martinek, Jessica Martin, Cédric Belair, Matthew J. Payea +3 more
2023bioRxiv3 citations Open access
Semantic Scholar
Economic crisis in Greece: The invisible enemy of blood donation or not?
S. Fortis, Anastasios G. Kriebardis, H. Georgatzakou, G. Lyrakos +5 more
2022Transfusion and Apheresis Science3 citations
Semantic Scholar
cCLIP-Seq: Retrieval of Chimeric Reads from HITS-CLIP (CLIP-Seq) Libraries.
Panagiotis Alexiou, Manolis Maragkakis, Z. Mourelatos, Anastassios Vourekas
2018Methods in molecular biology3 citations
Semantic Scholar
GenOO: A Modern Perl Framework for High Throughput Sequencing analysis
Manolis Maragkakis, Panagiotis Alexiou, Z. Mourelatos
2015bioRxiv3 citations Open access
Semantic Scholar
An improved neural network ensemble model of Aldose Reductase inhibitory activity
B. K. Hedayati, R. Parra-Hernandez, E. M. Laxdal, N. Dimopoulos +2 more
2012IEEE International Joint Conference on Neural Network3 citations Open access
Semantic Scholar
Online resources for microRNA analysis
Panagiotis Alexiou, Manolis Maragkakis, A. Hatzigeorgiou
2011Journal of Nucleic Acids Investigation3 citations Open access
Semantic Scholar

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