Nikolaos Alachiotis

According to our database, Nikolaos Alachiotis authored at least 53 papers between 2009 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2023

A Survey of Processing Systems for Phylogenetics and Population Genetics.

Reinout Corts, Nikolaos Alachiotis

ACM Trans. Reconfigurable Technol. Syst., September, 2023

Genome-wide scans for selective sweeps using convolutional neural networks.

Hanqing Zhao, Matthijs Leon Souilljee, Pavlos Pavlidis, Nikolaos Alachiotis

Bioinform., 2023

SweepNet: A Lightweight CNN Architecture for the Classification of Adaptive Genomic Regions.

Hanqing Zhao, Pavlos Pavlidis, Nikolaos Alachiotis

Proceedings of the Platform for Advanced Scientific Computing Conference, 2023

Accelerated Real-Time Classification of Evolving Data Streams using Adaptive Random Forests.

Frank Ridder, Kuan-Hsun Chen, Nikolaos Alachiotis

Proceedings of the International Conference on Field Programmable Technology, 2023

FPGA-accelerated Quantum Transport Measurements.

Timo Haarman, Antonio Sousa de Almeida, Amber Heskes, Floris Zwanenburg, Nikolaos Alachiotis

Proceedings of the International Conference on Field Programmable Technology, 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, Marco Ottavi

Proceedings of the IEEE European Test Symposium, 2023

Exploring Genomic Sequence Alignment for Improving Side-Channel Analysis.

Heitor Uchoa, Vipul Arora, Dennis Vermoen, Marco Ottavi, Nikolaos Alachiotis

Proceedings of the Computer Security - ESORICS 2023, 2023

Neutron Radiation Tests of the NEORV32 RISC-V SoC on Flash-Based FPGAs.

Kevin Böhmer, Bruno Forlin, Carlo Cazzaniga, Paolo Rech, Gianluca Furano, Nikolaos Alachiotis, Marco Ottavi

Proceedings of the IEEE International Symposium on Defect and Fault Tolerance in VLSI and Nanotechnology Systems, 2023

Effective Data Preprocessing Techniques for CNN-based Selective Sweep Detection.

Hanqing Zhao, Nikolaos Alachiotis

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022

Scalable Phylogeny Reconstruction with Disaggregated Near-memory Processing.

Nikolaos Alachiotis, Panagiotis Skrimponis, Manolis Pissadakis, Dionisios N. Pnevmatikatos

ACM Trans. Reconfigurable Technol. Syst., 2022

A novel approximation scheme for floating-point square root and inverse square root for FPGAs.

Pietro Pennestrì, Yanqiu Huang, Nikolaos Alachiotis

Proceedings of the 11th International Conference on Modern Circuits and Systems Technologies, 2022

Accelerated LD-based selective sweep detection using GPUs and FPGAs.

Reinout Corts, Niek Sterenborg, Nikolaos Alachiotis

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

An Event-driven Recurrent Spiking Neural Network Architecture for Efficient Inference on FPGA.

Anand Sankaran, Paul Detterer, Kalpana Kannan, Nikolaos Alachiotis, Federico Corradi

Proceedings of the ICONS 2022: International Conference on Neuromorphic Systems, Knoxville, TN, USA, July 27, 2022

2021

Accelerating Phylogenetics Using FPGAs in the Cloud.

Nikolaos Alachiotis, Andreas Brokalakis, Vasilis Amourgianos, Sotiris Ioannidis, Pavlos Malakonakis, Tasos Bokalidis

IEEE Micro, 2021

An Energy-Efficient FPGA-based Convolutional Neural Network Implementation.

Hasan Irmak, Nikolaos Alachiotis, Daniel Ziener

Proceedings of the 29th Signal Processing and Communications Applications Conference, 2021

EDRA: A Hardware-Assisted Decoupled Access/Execute Framework on the Digital Market - Invited Paper.

Dimitris Theodoropoulos, Andreas Brokalakis, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos

Proceedings of the Embedded Computer Systems: Architectures, Modeling, and Simulation, 2021

Increasing Flexibility of FPGA-based CNN Accelerators with Dynamic Partial Reconfiguration.

Hasan Irmak, Daniel Ziener, Nikolaos Alachiotis

Proceedings of the 31st International Conference on Field-Programmable Logic and Applications, 2021

Integrative hierarchical ensemble clustering for improved disease subtype discovery.

Bastian Pfeifer, Andrei Voicu-Spineanu, Michael G. Schimek, Nikolaos Alachiotis

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020

RAiSD-X: A Fast and Accurate FPGA System for the Detection of Positive Selection in Thousands of Genomes.

Nikolaos Alachiotis, Charalampos Vatsolakis, Grigorios Chrysos, Dionisios N. Pnevmatikatos

ACM Trans. Reconfigurable Technol. Syst., 2020

Near-memory Acceleration for Scalable Phylogenetic Inference.

Nikolaos Alachiotis, Panagiotis Skrimponis, Emmanouil Pissadakis, Sundeep Rangan, Dionisios N. Pnevmatikatos

Proceedings of the FPGA '20: The 2020 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays, 2020

qLD: High-performance Computation of Linkage Disequilibrium on CPU and GPU.

Charalampos Theodoris, Nikolaos Alachiotis, Tze Meng Low, Pavlos Pavlidis

Proceedings of the 20th IEEE International Conference on Bioinformatics and Bioengineering, 2020

Exploring Modern FPGA Platforms for Faster Phylogeny Reconstruction with RAxML.

Pavlos Malakonakis, Andreas Brokalakis, Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas

Proceedings of the 20th IEEE International Conference on Bioinformatics and Bioengineering, 2020

2019

Accelerating Binarized Convolutional Neural Networks with Dynamic Partial Reconfiguration on Disaggregated FPGAs.

Panagiotis Skrimponis, Emmanouil Pissadakis, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos

Proceedings of the Parallel Computing: Technology Trends, 2019

2018

ReFiRe: Efficient Deployment of Remote Fine-Grained Reconfigurable Accelerators.

Emmanouil Pissadakis, Nikolaos Alachiotis, Panagiotis Skrimponis, Dimitris Theodoropoulos, Thanasis Korakis, Dionisios N. Pnevmatikatos

Proceedings of the International Conference on Field-Programmable Technology, 2018

Accelerated Inference of Positive Selection on Whole Genomes.

Nikolaos Alachiotis, Charalampos Vatsolakis, Grigorios Chrysos, Dionisios N. Pnevmatikatos

Proceedings of the 28th International Conference on Field Programmable Logic and Applications, 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, Dionisis N. Pnevmatikatos, E. H. Pap, George Zervas, Vaibhawa Mishra, Arsalan Saljoghei, Alvise Rigo, Jose Fernando Zazo, Sergio López-Buedo, Martí Torrents, Ferad Zyulkyarov, Michael Enrico, Óscar González de Dios

Proceedings of the 2018 Design, Automation & Test in Europe Conference & Exhibition, 2018

REMAP: Remote mEmory Manager for disAggregated Platforms.

Dimitris Theodoropoulos, Andrea Reale, Dimitris Syrivelis, Maciej Bielski, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos

Proceedings of the 29th IEEE International Conference on Application-specific Systems, 2018

2017

FPGA-based evaluation platform for disaggregated computing.

Dimitris Theodoropoulos, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos

Proceedings of the 2017 International Conference on Embedded Computer Systems: Architectures, 2017

Deploying FPGAs to future-proof genome-wide analyses based on linkage disequilibrium.

Dimitrios Bozikas, Nikolaos Alachiotis, Pavlos Pavlidis, Euripides Sotiriades, Apostolos Dollas

Proceedings of the 27th International Conference on Field Programmable Logic and Applications, 2017

Versatile deployment of FPGA accelerators in disaggregated data centers: A bioinformatics case study.

Nikolaos Alachiotis, Dimitris Theodoropoulos, Dionisios N. Pnevmatikatos

Proceedings of the 27th International Conference on Field Programmable Logic and Applications, 2017

Multi-FPGA Evaluation Platform for Disaggregated Computing.

Dimitris Theodoropoulos, Nikolaos Alachiotis, Dionisios N. Pnevmatikatos

Proceedings of the 25th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines, 2017

2016

Efficient Computation of Linkage Disequilibria as Dense Linear Algebra Operations.

Nikolaos Alachiotis, Doru-Thom Popovici, Tze Meng Low

Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016

High Performance Linkage Disequilibrium: FPGAs Hold the Key.

Nikolaos Alachiotis, Gabriel Weisz

Proceedings of the 2016 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays, 2016

2015

Enabling portable energy efficiency with memory accelerated library.

Qi Guo, Tze Meng Low, Nikolaos Alachiotis, Berkin Akin, Larry T. Pileggi, James C. Hoe, Franz Franchetti

Proceedings of the 48th International Symposium on Microarchitecture, 2015

Generating FPGA accelerators for chemical similarity assessment.

Nikolaos Alachiotis

Proceedings of the 25th International Conference on Field Programmable Logic and Applications, 2015

2013

libgapmis: extending short-read alignments.

Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

BMC Bioinform., 2013

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library.

Fernando Izquierdo-Carrasco, Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

2012

Algorithms and Computer Architectures for Evolutionary Bioinformatics.

Nikolaos Alachiotis

PhD thesis, 2012

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.

Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis

BMC Bioinform., 2012

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets.

Nikolaos Alachiotis, Alexandros Stamatakis, Pavlos Pavlidis

Bioinform., 2012

A versatile UDP/IP based PC ↔ FPGA communication platform.

Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis

Proceedings of the 2012 International Conference on Reconfigurable Computing and FPGAs, 2012

An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data.

Simon A. Berger, Nikolaos Alachiotis, Alexandros Stamatakis

Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012

Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection.

Nikolaos Alachiotis, Pavlos Pavlidis, Alexandros Stamatakis

Proceedings of the Algorithms and Architectures for Parallel Processing, 2012

Libgapmis: An ultrafast library for short-read single-gap alignment.

Nikolaos Alachiotis, Simon A. Berger, Tomás Flouri, Solon P. Pissis, Alexandros Stamatakis

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011

A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm.

Nikolaos Alachiotis, Alexandros Stamatakis

Int. J. Reconfigurable Comput., 2011

FPGA Acceleration of the Phylogenetic Parsimony Kernel?

Nikolaos Alachiotis, Alexandros Stamatakis

Proceedings of the International Conference on Field Programmable Logic and Applications, 2011

Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs.

Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis

Proceedings of the IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, 2011

FPGA Optimizations for a Pipelined Floating-Point Exponential Unit.

Nikolaos Alachiotis, Alexandros Stamatakis

Proceedings of the Reconfigurable Computing: Architectures, Tools and Applications, 2011

2010

Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data.

Alexandros Stamatakis, Nikolaos Alachiotis

Bioinform., 2010

Efficient floating-point logarithm unit for FPGAs.

Nikolaos Alachiotis, Alexandros Stamatakis

Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010

Efficient PC-FPGA Communication over Gigabit Ethernet.

Nikolaos Alachiotis, Simon A. Berger, Alexandros Stamatakis

Proceedings of the 10th IEEE International Conference on Computer and Information Technology, 2010

2009

Exploring FPGAs for accelerating the phylogenetic likelihood function.

Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas, Alexandros Stamatakis

Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

A reconfigurable architecture for the Phylogenetic Likelihood Function.

Nikolaos Alachiotis, Alexandros Stamatakis, Euripides Sotiriades, Apostolos Dollas

Proceedings of the 19th International Conference on Field Programmable Logic and Applications, 2009