Individualized markers optimize class prediction of microarray data. - Pavlos Pavlidis; Panayiota Poirazi (BMC Bioinform., 2006)

Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection. - Nikolaos Alachiotis 001; Pavlos Pavlidis; Alexandros Stamatakis (ICA3PP (1), 2012)

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. - Nikolaos Alachiotis 001; Alexandros Stamatakis; Pavlos Pavlidis (Bioinform., 2012)

MoTeX: A word-based HPC tool for MoTif eXtraction. - Solon P. Pissis; Alexandros Stamatakis; Pavlos Pavlidis (BCB, 2013)

Accelerating String Matching on MIC Architecture for Motif Extraction. - Solon P. Pissis; Christian Goll; Pavlos Pavlidis; Alexandros Stamatakis (PPAM (2), 2013)

A general species delimitation method with applications to phylogenetic placements. - Jiajie Zhang; Paschalia Kapli; Pavlos Pavlidis; Alexandros Stamatakis (Bioinform., 2013)

1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans. - Marc Pybus; Giovanni Marco Dall'Olio; Pierre Luisi; Manu Uzkudun; Angel Carreño-Torres; Pavlos Pavlidis; Hafid Laayouni; Jaume Bertranpetit; Johannes Engelken (Nucleic Acids Res., 2014)

Deploying FPGAs to future-proof genome-wide analyses based on linkage disequilibrium. - Dimitrios Bozikas; Nikolaos Alachiotis 001; Pavlos Pavlidis; Euripides Sotiriades; Apostolos Dollas (FPL, 2017)

Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. - Paschalia Kapli; Sarah Lutteropp; Jiajie Zhang; Kassian Kobert; Pavlos Pavlidis; Alexandros Stamatakis; Tomás Flouri (Bioinform., 2017)

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. - Duo Xu; Yousef Jaber; Pavlos Pavlidis; Omer Gokcumen (BMC Bioinform., 2017)

qLD: High-performance Computation of Linkage Disequilibrium on CPU and GPU. - Charalampos Theodoris; Nikolaos Alachiotis 001; Tze Meng Low; Pavlos Pavlidis (BIBE, 2020)

Efficient Dynamic Analysis of Low-similarity Proteins for Structural Class Prediction. - Michaela Areti Zervou; Effrosyni Doutsi; Pavlos Pavlidis; Panagiotis Tsakalides (EUSIPCO, 2020)

Structural classification of proteins based on the computationally efficient recurrence quantification analysis and horizontal visibility graphs. - Michaela Areti Zervou; Effrosyni Doutsi; Pavlos Pavlidis; Panagiotis Tsakalides (Bioinform., 2021)

Cronos: A Machine Learning Pipeline for Description and Predictive Modeling of Microbial Communities Over Time. - Aristeidis Litos; Evangelia Intze; Pavlos Pavlidis; Ilias Lagkouvardos (Frontiers Bioinform., 2022)

SweepNet: A Lightweight CNN Architecture for the Classification of Adaptive Genomic Regions. - Hanqing Zhao; Pavlos Pavlidis; Nikolaos Alachiotis 001 (PASC, 2023)

Genome-wide scans for selective sweeps using convolutional neural networks. - Hanqing Zhao; Matthijs Leon Souilljee; Pavlos Pavlidis; Nikolaos Alachiotis 001 (Bioinform., 2023)