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Jan Fostier

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affiliation: Ghent University, Belgium

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2020 – today

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2024
[c10]
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Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro:
Faster Maximal Exact Matches with Lazy LCP Evaluation. DCC 2024: 123-132
[c9]
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Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier:
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. RECOMB 2024: 164-184
[c8]
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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: 10:1-10:18
2023
[j18]
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Lore Depuydt, Luca Renders, Thomas Abeel, Jan Fostier:
Pan-genome de Bruijn graph using the bidirectional FM-index. BMC Bioinform. 24(1): 400 (2023)
[j17]
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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): 1995-2006 (2023)
[c7]
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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: 1205-1209
[i1]
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  - journals/corr/abs-2311-04538
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Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro:
Faster Maximal Exact Matches with Lazy LCP Evaluation. CoRR abs/2311.04538 (2023)
2022
[c6]
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Luca Renders, Lore Depuydt, Jan Fostier:
Approximate Pattern Matching Using Search Schemes and In-Text Verification. IWBBIO (2) 2022: 419-435
2020
[j16]
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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): 2275-2277 (2020)
[j15]
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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): 402 (2020)

2010 – 2019

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2019
[j14]
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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): 298:1-298:13 (2019)
2018
[j13]
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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): 311:1-311:10 (2018)
[j12]
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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)
[c5]
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Jan Fostier:
A BLAS-Based Algorithm for Finding Position Weight Matrix Occurrences in DNA Sequences on CPUs and GPUs. IWBBIO (1) 2018: 439-449
2017
[j11]
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Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier:
OMSim: a simulator for optical map data. Bioinform. 33(17): 2740-2742 (2017)
[j10]
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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): 374:1-374:13 (2017)
2016
[j9]
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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: 10 (2016)
2015
[j8]
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Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier:
Halvade: scalable sequence analysis with MapReduce. Bioinform. 31(15): 2482-2488 (2015)
[j7]
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Dieter De Witte, Jan Van de Velde, Dries Decap, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier:
BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements. Bioinform. 31(23): 3758-3766 (2015)
[c4]
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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: 747-750
[c3]
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Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier:
Performance Analysis of a Parallel, Multi-node Pipeline for DNA Sequencing. PPAM (2) 2015: 233-242
[c2]
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Giles Miclotte, Mahdi Heydari, Piet Demeester, Pieter Audenaert, Jan Fostier:
Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches. WABI 2015: 175-188
2014
[j6]
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Simon Dooms, Pieter Audenaert, Jan Fostier, Toon De Pessemier, Luc Martens:
In-memory, distributed content-based recommender system. J. Intell. Inf. Syst. 42(3): 645-669 (2014)
2013
[j5]
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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): 1308-1316 (2013)
[c1]
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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: 268-277
2012
[j4]
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I. Bogaert, B. Michiels, Jan Fostier:
O(1) Computation of Legendre Polynomials and Gauss-Legendre Nodes and Weights for Parallel Computing. SIAM J. Sci. Comput. 34(3) (2012)
[j3]
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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): 768-786 (2012)
2011
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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): 749-756 (2011)

2000 – 2009

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2007
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Jan Fostier, Femke Olyslager:
A GRID Computer Implementation of the Multilevel Fast Multipole Algorithm for Full-Wave Analysis of Optical Devices. IEICE Trans. Commun. 90-B(9): 2430-2438 (2007)

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