A reconfigurable architecture for the Phylogenetic Likelihood Function. - Nikolaos Alachiotis 001; Alexandros Stamatakis; Euripides Sotiriades; Apostolos Dollas (FPL, 2009)

Exploring FPGAs for accelerating the phylogenetic likelihood function. - Nikolaos Alachiotis 001; Euripides Sotiriades; Apostolos Dollas; Alexandros Stamatakis (IPDPS, 2009)

Efficient PC-FPGA Communication over Gigabit Ethernet. - Nikolaos Alachiotis 001; Simon A. Berger; Alexandros Stamatakis (CIT, 2010)

Efficient floating-point logarithm unit for FPGAs. - Nikolaos Alachiotis 001; Alexandros Stamatakis (IPDPS Workshops, 2010)

Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data. - Alexandros Stamatakis; Nikolaos Alachiotis 001 (Bioinform., 2010)

FPGA Optimizations for a Pipelined Floating-Point Exponential Unit. - Nikolaos Alachiotis 001; Alexandros Stamatakis (ARC, 2011)

Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs. - Nikolaos Alachiotis 001; Simon A. Berger; Alexandros Stamatakis (FCCM, 2011)

FPGA Acceleration of the Phylogenetic Parsimony Kernel? - Nikolaos Alachiotis 001; Alexandros Stamatakis (FPL, 2011)

A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm. - Nikolaos Alachiotis 001; Alexandros Stamatakis (Int. J. Reconfigurable Comput., 2011)

Libgapmis: An ultrafast library for short-read single-gap alignment. - Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (BIBM Workshops, 2012)

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

An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data. - Simon A. Berger; Nikolaos Alachiotis 001; Alexandros Stamatakis (IPDPS Workshops, 2012)

A versatile UDP/IP based PC ↔ FPGA communication platform. - Nikolaos Alachiotis 001; Simon A. Berger; Alexandros Stamatakis (ReConFig, 2012)

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

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel. - Nikolaos Alachiotis 001; Simon A. Berger; Alexandros Stamatakis (BMC Bioinform., 2012)

Algorithms and Computer Architectures for Evolutionary Bioinformatics. - Nikolaos Alachiotis 001 (2012)

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library. - Fernando Izquierdo-Carrasco; Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (IPDPS Workshops, 2013)

libgapmis: extending short-read alignments. - Nikolaos Alachiotis 001; Simon A. Berger; Tomás Flouri; Solon P. Pissis; Alexandros Stamatakis (BMC Bioinform., 2013)

Generating FPGA accelerators for chemical similarity assessment. - Nikolaos Alachiotis 001 (FPL, 2015)

Enabling portable energy efficiency with memory accelerated library. - Qi Guo 001; Tze Meng Low; Nikolaos Alachiotis 001; Berkin Akin; Larry T. Pileggi; James C. Hoe; Franz Franchetti (MICRO, 2015)

High Performance Linkage Disequilibrium: FPGAs Hold the Key. - Nikolaos Alachiotis 001; Gabriel Weisz (FPGA, 2016)

Efficient Computation of Linkage Disequilibria as Dense Linear Algebra Operations. - Nikolaos Alachiotis 001; Doru-Thom Popovici; Tze Meng Low (IPDPS Workshops, 2016)

Multi-FPGA Evaluation Platform for Disaggregated Computing. - Dimitris Theodoropoulos; Nikolaos Alachiotis 001; Dionisios N. Pnevmatikatos (FCCM, 2017)

Versatile deployment of FPGA accelerators in disaggregated data centers: A bioinformatics case study. - Nikolaos Alachiotis 001; Dimitris Theodoropoulos; Dionisios N. Pnevmatikatos (FPL, 2017)

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)

FPGA-based evaluation platform for disaggregated computing. - Dimitris Theodoropoulos; Nikolaos Alachiotis 001; Dionisios N. Pnevmatikatos (SAMOS, 2017)

REMAP: Remote mEmory Manager for disAggregated Platforms. - Dimitris Theodoropoulos; Andrea Reale; Dimitris Syrivelis; Maciej Bielski; Nikolaos Alachiotis 001; Dionisios N. Pnevmatikatos (ASAP, 2018)

dReDBox: Materializing a full-stack rack-scale system prototype of a next-generation disaggregated datacenter. - Maciej Bielski; Ilias Syrigos; Kostas Katrinis; Dimitris Syrivelis; Andrea Reale; Dimitris Theodoropoulos; Nikolaos Alachiotis 001; Dionisis N. Pnevmatikatos; E. H. Pap; George Zervas; Vaibhawa Mishra; Arsalan Saljoghei; et al. (DATE, 2018)

Accelerated Inference of Positive Selection on Whole Genomes. - Nikolaos Alachiotis 001; Charalampos Vatsolakis; Grigorios Chrysos 001; Dionisios N. Pnevmatikatos (FPL, 2018)

ReFiRe: Efficient Deployment of Remote Fine-Grained Reconfigurable Accelerators. - Emmanouil Pissadakis; Nikolaos Alachiotis 001; Panagiotis Skrimponis; Dimitris Theodoropoulos; Thanasis Korakis; Dionisios N. Pnevmatikatos (FPT, 2018)

Accelerating Binarized Convolutional Neural Networks with Dynamic Partial Reconfiguration on Disaggregated FPGAs. - Panagiotis Skrimponis; Emmanouil Pissadakis; Nikolaos Alachiotis 001; Dionisios N. Pnevmatikatos (PARCO, 2019)

Exploring Modern FPGA Platforms for Faster Phylogeny Reconstruction with RAxML. - Pavlos Malakonakis; Andreas Brokalakis; Nikolaos Alachiotis 001; Euripides Sotiriades; Apostolos Dollas (BIBE, 2020)

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

Near-memory Acceleration for Scalable Phylogenetic Inference. - Nikolaos Alachiotis 001; Panagiotis Skrimponis; Emmanouil Pissadakis; Sundeep Rangan; Dionisios N. Pnevmatikatos (FPGA, 2020)

RAiSD-X: A Fast and Accurate FPGA System for the Detection of Positive Selection in Thousands of Genomes. - Nikolaos Alachiotis 001; Charalampos Vatsolakis; Grigorios Chrysos 001; Dionisios N. Pnevmatikatos (ACM Trans. Reconfigurable Technol. Syst., 2020)

Integrative hierarchical ensemble clustering for improved disease subtype discovery. - Bastian Pfeifer; Andrei Voicu-Spineanu; Michael G. Schimek; Nikolaos Alachiotis 001 (BIBM, 2021)

Increasing Flexibility of FPGA-based CNN Accelerators with Dynamic Partial Reconfiguration. - Hasan Irmak; Daniel Ziener; Nikolaos Alachiotis 001 (FPL, 2021)

EDRA: A Hardware-Assisted Decoupled Access/Execute Framework on the Digital Market - Invited Paper. - Dimitris Theodoropoulos; Andreas Brokalakis; Nikolaos Alachiotis 001; Dionisios N. Pnevmatikatos (SAMOS, 2021)

An Energy-Efficient FPGA-based Convolutional Neural Network Implementation. - Hasan Irmak; Nikolaos Alachiotis 001; Daniel Ziener (SIU, 2021)

Accelerating Phylogenetics Using FPGAs in the Cloud. - Nikolaos Alachiotis 001; Andreas Brokalakis; Vasilis Amourgianos; Sotiris Ioannidis; Pavlos Malakonakis; Tasos Bokalidis (IEEE Micro, 2021)

An Event-driven Recurrent Spiking Neural Network Architecture for Efficient Inference on FPGA. - Anand Sankaran; Paul Detterer; Kalpana Kannan; Nikolaos Alachiotis 001; Federico Corradi (ICONS, 2022)

Accelerated LD-based selective sweep detection using GPUs and FPGAs. - Reinout Corts; Niek Sterenborg; Nikolaos Alachiotis 001 (IPDPS Workshops, 2022)

A novel approximation scheme for floating-point square root and inverse square root for FPGAs. - Pietro Pennestrì; Yanqiu Huang; Nikolaos Alachiotis 001 (MOCAST, 2022)

Scalable Phylogeny Reconstruction with Disaggregated Near-memory Processing. - Nikolaos Alachiotis 001; Panagiotis Skrimponis; Manolis Pissadakis; Dionisios N. Pnevmatikatos (ACM Trans. Reconfigurable Technol. Syst., 2022)

Effective Data Preprocessing Techniques for CNN-based Selective Sweep Detection. - Hanqing Zhao; Nikolaos Alachiotis 001 (BIBM, 2023)

Neutron Radiation Tests of the NEORV32 RISC-V SoC on Flash-Based FPGAs. - Kevin Böhmer; Bruno Endres Forlin; Carlo Cazzaniga; Paolo Rech; Gianluca Furano; Nikolaos Alachiotis 001; Marco Ottavi (DFT, 2023)

Exploring Genomic Sequence Alignment for Improving Side-Channel Analysis. - Heitor Uchoa; Vipul Arora 004; Dennis Vermoen; Marco Ottavi; Nikolaos Alachiotis 001 (ESORICS (3), 2023)

An unprotected RISC-V Soft-core processor on an SRAM FPGA: Is it as bad as it sounds? - Bruno E. Forlin; Wouter van Huffelen; Carlo Cazzaniga; Paolo Rech; Nikolaos Alachiotis 001; Marco Ottavi (ETS, 2023)

FPGA-accelerated Quantum Transport Measurements. - Timo Haarman; António J. Sousa de Almeida; Amber Heskes; Floris Zwanenburg; Nikolaos Alachiotis 001 (ICFPT, 2023)

Accelerated Real-Time Classification of Evolving Data Streams using Adaptive Random Forests. - Frank Ridder; Kuan-Hsun Chen; Nikolaos Alachiotis 001 (ICFPT, 2023)

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)

A Survey of Processing Systems for Phylogenetics and Population Genetics. - Reinout Corts; Nikolaos Alachiotis 001 (ACM Trans. Reconfigurable Technol. Syst., 2023)

Lightweight Instrumentation for Accurate Performance Monitoring in RTOSes. - Bruno Endres Forlin; Kuan-Hsun Chen; Nikolaos Alachiotis 001; Luca Cassano; Marco Ottavi (DATE, 2024)

Exploring the Versal AI Engines for Signal Processing in Radio Astronomy. - Victor Van Wijhe; Vincent Sprave; Daniele Passaretti; Nikolaos Alachiotis 001; Gerrit Grutzeck; Thilo Pionteck; Steven van der Vlugt (FPL, 2024)

Accelerated Spiking Convolutional Neural Networks for Scalable Population Genomics. - Federico Corradi; Zhanbo Shen; Hanqing Zhao; Nikolaos Alachiotis 001 (HEART, 2024)

SoftCache: A Software Cache for PCIe-Attached Hardware Accelerators. - Steven Wijnja; Nikolaos Alachiotis 001 (PASC, 2024)

Scalable CNN-based classification of selective sweeps using derived allele frequencies. - Sjoerd van den Belt; Hanqing Zhao; Nikolaos Alachiotis 001 (Bioinform., 2024)

Exploring the AMD® Deep Learning Processor Unit for Accelerating Selective Sweep Detection. - Nikolaos Alachiotis 001; Matthijs Leon Souilljee (IPDPS (Workshops), 2025)

Accelerated CNN-based Scans for Traces of Positive Selection. - Sjoerd van den Belt; Nikolaos Alachiotis 001 (PASC, 2025)

FPGA Innovation Research in the Netherlands: Present Landscape and Future Outlook. - Nikolaos Alachiotis 001; Sjoerd van den Belt; Steven van der Vlugt; Reinier van der Walle; Mohsen Safari; Bruno Endres Forlin; Tiziano De Matteis; Zaid Al-Ars; Roel Jordans; António J. Sousa de Almeida; Federico Corradi; Christiaan Baaij; et al. (CoRR, 2025)