Jan Fostier

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 18

Top Topics

Efficient Search

Error Correction

Approximate Pattern Matching

Top Venues

Publications

Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
Faster Maximal Exact Matches with Lazy LCP Evaluation. DCC (2024)
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. RECOMB (2024)
Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier
b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index. WABI (2024)
Pratima Upretee, Sybren Santermans, Koen M. Martens, Juliette Gevers, Sanjin Marion, Wouter Van den Bosch, Jan Fostier, Nilesh Madhu
Detecting Translocation of DNA Nanostructures Through Nanopores: First Steps Towards Structural Barcode Readout. EUSIPCO (2023)
Aranka Steyaert, Pieter Audenaert, Jan Fostier
Improved Node and Arc Multiplicity Estimation in De Bruijn Graphs Using Approximate Inference in Conditional Random Fields. IEEE ACM Trans. Comput. Biol. Bioinform. 20 (3) (2023)
Lore Depuydt, Luca Renders, Thomas Abeel, Jan Fostier
Pan-genome de Bruijn graph using the bidirectional FM-index. BMC Bioinform. 24 (1) (2023)
Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
Faster Maximal Exact Matches with Lazy LCP Evaluation. CoRR (2023)
Omar Ahmed, Andrej Baláz, Nathaniel K. Brown, Lore Depuydt, Adrián Goga, Alessia Petescia, Mohsen Zakeri, Jan Fostier, Travis Gagie, Ben Langmead, Gonzalo Navarro, Nicola Prezza
r-indexing without backward searching. CoRR (2023)
Luca Renders, Lore Depuydt, Jan Fostier
Approximate Pattern Matching Using Search Schemes and In-Text Verification. IWBBIO (2) (2022)
Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez
GABAC: an arithmetic coding solution for genomic data. Bioinform. 36 (7) (2020)
Aranka Steyaert, Pieter Audenaert, Jan Fostier
Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields. BMC Bioinform. 21 (1) (2020)
Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
Illumina error correction near highly repetitive DNA regions improves de novo genome assembly. BMC Bioinform. 20 (1) (2019)
Nele Vandersickel, Masaya Watanabe, Qian Tao, Jan Fostier, Katja Zeppenfeld, Alexander V. Panfilov
Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern. PLoS Comput. Biol. 14 (12) (2018)
Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs. BMC Bioinform. 19 (1) (2018)
Jan Fostier
A BLAS-Based Algorithm for Finding Position Weight Matrix Occurrences in DNA Sequences on CPUs and GPUs. IWBBIO (1) (2018)
Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
Evaluation of the impact of Illumina error correction tools on de novo genome assembly. BMC Bioinform. 18 (1) (2017)
Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
OMSim: a simulator for optical map data. Bioinform. 33 (17) (2017)
Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
Jabba: hybrid error correction for long sequencing reads. Algorithms Mol. Biol. 11 (2016)
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
Performance Analysis of a Parallel, Multi-node Pipeline for DNA Sequencing. PPAM (2) (2015)
Arne De Coninck, Drosos Kourounis, Fabio Verbosio, Olaf Schenk, Bernard De Baets, Steven Maenhout, Jan Fostier
Towards Parallel Large-Scale Genomic Prediction by Coupling Sparse and Dense Matrix Algebra. PDP (2015)
Dieter De Witte, Jan Van de Velde, Dries Decap, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier
-regulatory elements. Bioinform. 31 (23) (2015)
Giles Miclotte, Mahdi Heydari, Piet Demeester, Pieter Audenaert, Jan Fostier
Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches. WABI (2015)
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
Halvade: scalable sequence analysis with MapReduce. Bioinform. 31 (15) (2015)
Simon Dooms, Pieter Audenaert, Jan Fostier, Toon De Pessemier, Luc Martens
In-memory, distributed content-based recommender system. J. Intell. Inf. Syst. 42 (3) (2014)
Lieven P. C. Verbeke, Lore Cloots, Piet Demeester, Jan Fostier, Kathleen Marchal
EPSILON: an eQTL prioritization framework using similarity measures derived from local networks. Bioinform. 29 (10) (2013)
Dieter De Witte, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier
A Parallel, Distributed-Memory Framework for Comparative Motif Discovery. PPAM (2) (2013)
I. Bogaert, B. Michiels, Jan Fostier
(1) Computation of Legendre Polynomials and Gauss-Legendre Nodes and Weights for Parallel Computing. SIAM J. Sci. Comput. 34 (3) (2012)
Maria Chtepen, Filip H. A. Claeys, Bart Dhoedt, Filip De Turck, Jan Fostier, Piet Demeester, Peter A. Vanrolleghem
Online execution time prediction for computationally intensive applications with periodic progress updates. J. Supercomput. 62 (2) (2012)
Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists. Bioinform. 27 (6) (2011)
Jan Fostier, Femke Olyslager
A GRID Computer Implementation of the Multilevel Fast Multipole Algorithm for Full-Wave Analysis of Optical Devices. IEICE Trans. Commun. (9) (2007)