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1

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

Nikolaos Alachiotis, Simon A Berger, Alexandros Stamatakis

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 232 KB

english, 2012

2

Molecular diversity and selective sweeps in maize inbred lines adapted to African highlands

Wegary, Dagne, Teklewold, Adefris, Prasanna, Boddupalli M., Ertiro, Berhanu T., Alachiotis, Nikolaos, Negera, Demewez, Awas, Geremew, Abakemal, Demissew, Ogugo, Veronica, Gowda, Manje, Semagn, Kassa

Journal:

Scientific Reports

Year:

2019

Language:

english

File:

PDF, 2.76 MB

english, 2019

3

Genome scans for selection and introgression based on k ânearest neighbor techniques

Pfeifer, Bastian, Alachiotis, Nikolaos, Pavlidis, Pavlos, Schimek, Michael G.

Journal:

Molecular Ecology Resources

Year:

2020

File:

PDF, 8.91 MB

2020

4

[IEEE 2017 27th International Conference on Field Programmable Logic and Applications (FPL) - Ghent, Belgium (2017.9.4-2017.9.8)] 2017 27th International Conference on Field Programmable Logic and Applications (FPL) - Deploying FPGAs to future-proof genome-wide analyses based on linkage disequilibrium

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

Year:

2017

Language:

english

File:

PDF, 7.50 MB

english, 2017

5

RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors

Alachiotis, Nikolaos, Pavlidis, Pavlos

Journal:

Communications Biology

Year:

2018

Language:

english

File:

PDF, 1.24 MB

english, 2018

6

[IEEE Distributed Processing, Workshops and Phd Forum (IPDPSW) - Atlanta, GA, USA (2010.04.19-2010.04.23)] 2010 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW) - Efficient floating-point logarithm unit for FPGAs

Alachiotis, Nikolaos, Stamatakis, Alexandros

Year:

2010

Language:

english

File:

PDF, 212 KB

english, 2010

7

[IEEE 2010 IEEE 10th International Conference on Computer and Information Technology (CIT) - Bradford, United Kingdom (2010.06.29-2010.07.1)] 2010 10th IEEE International Conference on Computer and Information Technology - Efficient PC-FPGA Communication over Gigabit Ethernet

Alachiotis, Nikolaos, Berger, Simon A., Stamatakis, Alexandros

Year:

2010

Language:

english

File:

PDF, 326 KB

english, 2010

8

[IEEE 2012 26th IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) - Shanghai, China (2012.05.21-2012.05.25)] 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum - An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data

Berger, Simon A., Alachiotis, Nikolaos, Stamatakis, Alexandros

Year:

2012

Language:

english

File:

PDF, 383 KB

english, 2012

9

[IEEE 2017 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS) - Pythagorion, Greece (2017.7.17-2017.7.20)] 2017 International Conference on Embedded Computer Systems: Architectures, Modeling, and Simulation (SAMOS) - FPGA-based evaluation platform for disaggregated computing

Theodoropoulos, Dimitris, Alachiotis, Nikolaos, Pnevmatikatos, Dionisios

Year:

2017

Language:

english

File:

PDF, 421 KB

english, 2017

10

[IEEE 2018 28th International Conference on Field Programmable Logic and Applications (FPL) - Dublin, Ireland (2018.8.27-2018.8.31)] 2018 28th International Conference on Field Programmable Logic and Applications (FPL) - Accelerated Inference of Positive Selection on Whole Genomes

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

Year:

2018

Language:

english

File:

PDF, 253 KB

english, 2018

11

[IEEE 2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM) - Salt Lake City, UT, USA (2011.05.1-2011.05.3)] 2011 IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines - Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs

Alachiotis, Nikolaos, Berger, Simon A., Stamatakis, Alexandros

Year:

2011

Language:

english

File:

PDF, 247 KB

english, 2011

12

Scalable linkage-disequilibrium-based selective sweep detection: a performance guide

Alachiotis, Nikolaos, Pavlidis, Pavlos

Journal:

Year:

2016

Language:

english

File:

PDF, 1.99 MB

english, 2016

13

[ACM Press the 48th International Symposium - Waikiki, Hawaii (2015.12.05-2015.12.09)] Proceedings of the 48th International Symposium on Microarchitecture - MICRO-48 - Enabling portable energy efficiency with memory accelerated library

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

Year:

2015

Language:

english

File:

PDF, 499 KB

english, 2015

14

A Methodology for Speeding Up Fast Fourier Transform Focusing on Memory Architecture Utilization

Kelefouras, Vasilios I., Athanasiou, George S., Alachiotis, Nikolaos, Michail, Harris E., Kritikakou, Angeliki S., Goutis, Costas E.

Journal:

IEEE Transactions on Signal Processing

Year:

2011

Language:

english

File:

PDF, 957 KB

english, 2011

15

RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors

Alachiotis, Nikolaos, Pavlidis, Pavlos

Journal:

Communications Biology

Year:

2018

File:

PDF, 1.24 MB

2018

16

[IEEE 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum (IPDPSW) - Cambridge, MA, USA (2013.05.20-2013.05.24)] 2013 IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum - A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library

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

Year:

2013

Language:

english

File:

PDF, 202 KB

english, 2013

17

[IEEE 2017 IEEE 25th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM) - Napa, CA, USA (2017.4.30-2017.5.2)] 2017 IEEE 25th Annual International Symposium on Field-Programmable Custom Computing Machines (FCCM) - Multi-FPGA Evaluation Platform for Disaggregated Computing

Theodoropoulos, Dimitris, Alachiotis, Nikolaos, Pnevmatikatos, Dionisios

Year:

2017

Language:

english

File:

PDF, 119 KB

english, 2017

18

[IEEE 2010 44th Asilomar Conference on Signals, Systems and Computers - Pacific Grove, CA, USA (2010.11.7-2010.11.10)] 2010 Conference Record of the Forty Fourth Asilomar Conference on Signals, Systems and Computers - A generic and versatile architecture for inference of evolutionary trees under maximum likelihood

Alachiotis, Nikolaos, Stamatakis, Alexandros

Year:

2010

Language:

english

File:

PDF, 135 KB

english, 2010

19

[IEEE 2018 IEEE 29th International Conference on Application-specific Systems, Architectures and Processors (ASAP) - Milano, Italy (2018.7.10-2018.7.12)] 2018 IEEE 29th International Conference on Application-specific Systems, Architectures and Processors (ASAP) - REMAP: Remote mEmory Manager for disAggregated Platforms

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

Year:

2018

Language:

english

File:

PDF, 2.15 MB

english, 2018

20

Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice

Ndjiondjop, Marie Noelle, Alachiotis, Nikolaos, Pavlidis, Pavlos, Goungoulou, Alphonse, Kpeki, Sèdjro Bienvenu, Zhao, Dule, Semagn, Kassa

Journal:

Theoretical and Applied Genetics

Year:

2018

Language:

english

File:

PDF, 1.18 MB

english, 2018

21

[IEEE 2018 International Conference on Field-Programmable Technology (FPT) - Naha, Okinawa, Japan (2018.12.10-2018.12.14)] 2018 International Conference on Field-Programmable Technology (FPT) - ReFiRe: Efficient Deployment of Remote Fine-Grained Reconfigurable Accelerators

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

Year:

2018

Language:

english

File:

PDF, 1.78 MB

english, 2018

22

A survey of methods and tools to detect recent and strong positive selection

Pavlos Pavlidis,Nikolaos Alachiotis

Journal:

Journal of Biological Research-Thessaloniki

Year:

2017

Language:

english

File:

PDF, 1.60 MB

english, 2017

23

[IEEE 2017 27th International Conference on Field Programmable Logic and Applications (FPL) - Ghent, Belgium (2017.9.4-2017.9.8)] 2017 27th International Conference on Field Programmable Logic and Applications (FPL) - Versatile deployment of FPGA accelerators in disaggregated data centers: A bioinformatics case study

Alachiotis, Nikolaos, Theodoropoulos, Dimitris, Pnevmatikatos, Dionisios

Year:

2017

Language:

english

File:

PDF, 251 KB

english, 2017

24

[IEEE 2012 International Conference on Reconfigurable Computing and FPGAs (ReConFig 2012) - Cancun, Mexico (2012.12.5-2012.12.7)] 2012 International Conference on Reconfigurable Computing and FPGAs - A versatile UDP/IP based PC ↔ FPGA communication platform

Alachiotis, Nikolaos, Berger, Simon A., Stamatakis, Alexandros

Year:

2012

Language:

english

File:

PDF, 91 KB

english, 2012

25

[IEEE 2009 International Conference on Field Programmable Logic and Applications (FPL) - Prague, Czech Republic (2009.08.31-2009.09.2)] 2009 International Conference on Field Programmable Logic and Applications - A reconfigurable architecture for the Phylogenetic Likelihood Function

Alachiotis, Nikolaos, Stamatakis, Alexandros, Sotiriades, Euripides, Dollas, Apostolos

Year:

2009

Language:

english

File:

PDF, 549 KB

english, 2009

26

[IEEE 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) - Chicago, IL, USA (2016.5.23-2016.5.27)] 2016 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW) - Efficient Computation of Linkage Disequilibria as Dense Linear Algebra Operations

Alachiotis, Nikolaos, Popovici, Thom, Low, Tze Meng

Year:

2016

Language:

english

File:

PDF, 291 KB

english, 2016

27

Decoupled Processors Architecture for Accelerating Data Intensive Applications using Scratch-Pad Memory Hierarchy

Athanasios Milidonis, Nikolaos Alachiotis, Vasileios Porpodas, Harris Michail, Georgios Panagiotakopoulos, Athanasios P. Kakarountas, Costas E. Goutis

Journal:

Journal of Signal Processing Systems

Year:

2010

Language:

english

File:

PDF, 317 KB

english, 2010

28

[IEEE 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) - Philadelphia, USA (2012.10.4-2012.10.7)] 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops - Libgapmis: An ultrafast library for short-read single-gap alignment

Alachiotis, Nikolaos, Berger, Simon, Flouri, Tomas, Pissis, Solon P., Stamatakis, Alexandras

Year:

2012

Language:

english

File:

PDF, 877 KB

english, 2012

29

[IEEE 2015 25th International Conference on Field Programmable Logic and Applications (FPL) - London, United Kingdom (2015.9.2-2015.9.4)] 2015 25th International Conference on Field Programmable Logic and Applications (FPL) - Generating FPGA accelerators for chemical similarity assessment

Alachiotis, Nikolaos

Year:

2015

Language:

english

File:

PDF, 146 KB

english, 2015

30

Archaic hominin introgression in Africa contributes to functional salivary MUC7 genetic variation

Xu, Duo, Pavlidis, Pavlos, Taskent, Recep Ozgur, Alachiotis, Nikolaos, Flanagan, Colin, DeGiorgio, Michael, Blekhman, Ran, Ruhl, Stefan, Gokcumen, Omer

Journal:

Molecular Biology and Evolution

Year:

2017

Language:

english

File:

PDF, 1.34 MB

english, 2017

31

libgapmis: extending short-read alignments

Alachiotis, Nikolaos, Berger, Simon, Flouri, Tomáš, Pissis, Solon P, Stamatakis, Alexandros

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 1.20 MB

english, 2013

32

[IEEE 2011 International Conference on Field Programmable Logic and Applications (FPL) - Chania, Greece (2011.09.5-2011.09.7)] 2011 21st International Conference on Field Programmable Logic and Applications - FPGA Acceleration of the Phylogenetic Parsimony Kernel?

Alachiotis, Nikolaos, Stamatakis, Alexandros

Year:

2011

Language:

english

File:

PDF, 219 KB

english, 2011

33

CHROMATOGATE: A TOOL FOR DETECTING BASE MIS-CALLS IN MULTIPLE SEQUENCE ALIGNMENTS BY SEMI-AUTOMATIC CHROMATOGRAM INSPECTION

Alachiotis, Nikolaos, Vogiatzi, Emmanouella, Pavlidis, Pavlos, Stamatakis, Alexandros

Journal:

Computational and Structural Biotechnology Journal

Year:

2013

Language:

english

File:

PDF, 3.54 MB

english, 2013

34

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

Alachiotis, Nikolaos, Stamatakis, Alexandros

Journal:

International Journal of Reconfigurable Computing

Year:

2011

Language:

english

File:

PDF, 1.51 MB

english, 2011

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