Jan Fostier

According to our database, Jan Fostier authored at least 29 papers between 2007 and 2024.

Collaborative distances:

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

2024

Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes.

Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier

J. Comput. Biol., 2024

b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index.

Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier

Proceedings of the 24th International Workshop on Algorithms in Bioinformatics, 2024

Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching.

Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier

Proceedings of the Research in Computational Molecular Biology, 2024

Faster Maximal Exact Matches with Lazy LCP Evaluation.

Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro

Proceedings of the Data Compression Conference, 2024

2023

Pan-genome de Bruijn graph using the bidirectional FM-index.

Lore Depuydt, Luca Renders, Thomas Abeel, Jan Fostier

BMC Bioinform., December, 2023

Improved Node and Arc Multiplicity Estimation in De Bruijn Graphs Using Approximate Inference in Conditional Random Fields.

Aranka Steyaert, Pieter Audenaert, Jan Fostier

IEEE ACM Trans. Comput. Biol. Bioinform., 2023

Detecting Translocation of DNA Nanostructures Through Nanopores: First Steps Towards Structural Barcode Readout.

Pratima Upretee, Sybren Santermans, Koen M. Martens, Juliette Gevers, Sanjin Marion, Wouter Van den Bosch, Jan Fostier, Nilesh Madhu

Proceedings of the 31st European Signal Processing Conference, 2023

2022

Approximate Pattern Matching Using Search Schemes and In-Text Verification.

Luca Renders, Lore Depuydt, Jan Fostier

Proceedings of the Bioinformatics and Biomedical Engineering, 2022

2020

Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields.

Aranka Steyaert, Pieter Audenaert, Jan Fostier

BMC Bioinform., 2020

GABAC: an arithmetic coding solution for genomic data.

Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez

Bioinform., 2020

2019

Illumina error correction near highly repetitive DNA regions improves de novo genome assembly.

Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier

BMC Bioinform., 2019

2018

Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern.

Nele Vandersickel, Masaya Watanabe, Qian Tao, Jan Fostier, Katja Zeppenfeld, Alexander V. Panfilov

PLoS Comput. Biol., 2018

BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs.

Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier

BMC Bioinform., 2018

A BLAS-Based Algorithm for Finding Position Weight Matrix Occurrences in DNA Sequences on CPUs and GPUs.

Jan Fostier

Proceedings of the Bioinformatics and Biomedical Engineering, 2018

2017

Evaluation of the impact of Illumina error correction tools on de novo genome assembly.

Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier

BMC Bioinform., 2017

OMSim: a simulator for optical map data.

Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier

Bioinform., 2017

2016

Jabba: hybrid error correction for long sequencing reads.

Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier

Algorithms Mol. Biol., 2016

2015

BLSSpeller: exhaustive comparative discovery of conserved <i>cis</i>-regulatory elements.

Dieter De Witte, Jan Van de Velde, Dries Decap, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier

Bioinform., 2015

Halvade: scalable sequence analysis with MapReduce.

Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier

Bioinform., 2015

Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches.

Giles Miclotte, Mahdi Heydari, Piet Demeester, Pieter Audenaert, Jan Fostier

Proceedings of the Algorithms in Bioinformatics - 15th International Workshop, 2015

Performance Analysis of a Parallel, Multi-node Pipeline for DNA Sequencing.

Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier

Proceedings of the Parallel Processing and Applied Mathematics, 2015

Towards Parallel Large-Scale Genomic Prediction by Coupling Sparse and Dense Matrix Algebra.

Arne De Coninck, Drosos Kourounis, Fabio Verbosio, Olaf Schenk, Bernard De Baets, Steven Maenhout, Jan Fostier

Proceedings of the 23rd Euromicro International Conference on Parallel, 2015

2014

In-memory, distributed content-based recommender system.

Simon Dooms, Pieter Audenaert, Jan Fostier, Toon De Pessemier, Luc Martens

J. Intell. Inf. Syst., 2014

2013

EPSILON: an eQTL prioritization framework using similarity measures derived from local networks.

Lieven P. C. Verbeke, Lore Cloots, Piet Demeester, Jan Fostier, Kathleen Marchal

Bioinform., 2013

A Parallel, Distributed-Memory Framework for Comparative Motif Discovery.

Dieter De Witte, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier

Proceedings of the Parallel Processing and Applied Mathematics, 2013

2012

Online execution time prediction for computationally intensive applications with periodic progress updates.

Maria Chtepen, Filip H. A. Claeys, Bart Dhoedt, Filip De Turck, Jan Fostier, Piet Demeester, Peter A. Vanrolleghem

J. Supercomput., 2012

<i>O</i>(1) Computation of Legendre Polynomials and Gauss-Legendre Nodes and Weights for Parallel Computing.

I. Bogaert, B. Michiels, Jan Fostier

SIAM J. Sci. Comput., 2012

2011

A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.

Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele

Bioinform., 2011

2007

A GRID Computer Implementation of the Multilevel Fast Multipole Algorithm for Full-Wave Analysis of Optical Devices.

Jan Fostier, Femke Olyslager

IEICE Trans. Commun., 2007