Jan Fostier

33 papers B 2C 3Journal 22Unranked 6
YearRankTypeTitle / Venue / Authors
2025 J jnl
Columba: fast approximate pattern matching with optimized search schemes.
Bioinform.
Luca Renders, Lore Depuydt, Travis Gagie, Jan Fostier
2025 J jnl
ELLIPSIS: robust quantification of splicing in scRNA-seq.
Bioinform.
Marie Van Hecke, Niko Beerenwinkel, Thibault Lootens, Jan Fostier, Robrecht Raedt, Kathleen Marchal
2025 — conf
Search Schemes for Approximate Pattern Matching: An Overview.
The Expanding World of Compressed Data
Lore Depuydt, Jan Fostier, Simon Gottlieb, Gregory Kucherov, Knut Reinert, Luca Renders
2025 J jnl
b-move: faster lossless approximate pattern matching in a run-length compressed index.
Algorithms Mol. Biol.
Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier
2024 B conf
Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching.
RECOMB
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
2024 B conf
Faster Maximal Exact Matches with Lazy LCP Evaluation.
DCC
Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
2024 J jnl
Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes.
J. Comput. Biol.
Luca Renders, Lore Depuydt, Sven Rahmann, Jan Fostier
2024 C conf
b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index.
WABI
Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, Jan Fostier
2023 — conf
Detecting Translocation of DNA Nanostructures Through Nanopores: First Steps Towards Structural Barcode Readout.
EUSIPCO
Pratima Upretee, Sybren Santermans, Koen M. Martens, Juliette Gevers, Sanjin Marion, Wouter Van den Bosch, Jan Fostier, Nilesh Madhu
2023 J jnl
Faster Maximal Exact Matches with Lazy LCP Evaluation.
CoRR
Adrián Goga, Lore Depuydt, Nathaniel K. Brown, Jan Fostier, Travis Gagie, Gonzalo Navarro
2023 J jnl
Improved Node and Arc Multiplicity Estimation in De Bruijn Graphs Using Approximate Inference in Conditional Random Fields.
IEEE ACM Trans. Comput. Biol. Bioinform.
Aranka Steyaert, Pieter Audenaert, Jan Fostier
2023 J jnl
Pan-genome de Bruijn graph using the bidirectional FM-index.
BMC Bioinform.
Lore Depuydt, Luca Renders, Thomas Abeel, Jan Fostier
2022 — conf
Approximate Pattern Matching Using Search Schemes and In-Text Verification.
IWBBIO (2)
Luca Renders, Lore Depuydt, Jan Fostier
2020 J jnl
Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields.
BMC Bioinform.
Aranka Steyaert, Pieter Audenaert, Jan Fostier
2020 J jnl
GABAC: an arithmetic coding solution for genomic data.
Bioinform.
Jan Voges, Tom Paridaens, Fabian Müntefering, Liudmila S. Mainzer, Brian Bliss, Mingyu Yang, Idoia Ochoa, Jan Fostier, Jörn Ostermann, Mikel Hernaez
2019 J jnl
Illumina error correction near highly repetitive DNA regions improves de novo genome assembly.
BMC Bioinform.
Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
2018 — conf
A BLAS-Based Algorithm for Finding Position Weight Matrix Occurrences in DNA Sequences on CPUs and GPUs.
IWBBIO (1)
Jan Fostier
2018 J jnl
BrownieAligner: accurate alignment of Illumina sequencing data to de Bruijn graphs.
BMC Bioinform.
Mahdi Heydari, Giles Miclotte, Yves Van de Peer, Jan Fostier
2018 J jnl
Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern.
PLoS Comput. Biol.
Nele Vandersickel, Masaya Watanabe, Qian Tao, Jan Fostier, Katja Zeppenfeld, Alexander V. Panfilov
2017 J jnl
Evaluation of the impact of Illumina error correction tools on de novo genome assembly.
BMC Bioinform.
Mahdi Heydari, Giles Miclotte, Piet Demeester, Yves Van de Peer, Jan Fostier
2017 J jnl
OMSim: a simulator for optical map data.
Bioinform.
Giles Miclotte, Stéphane Plaisance, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
2016 J jnl
Jabba: hybrid error correction for long sequencing reads.
Algorithms Mol. Biol.
Giles Miclotte, Mahdi Heydari, Piet Demeester, Stephane Rombauts, Yves Van de Peer, Pieter Audenaert, Jan Fostier
2015 J jnl
BLSSpeller: exhaustive comparative discovery of conserved
Bioinform.
Dieter De Witte, Jan Van de Velde, Dries Decap, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier
2015 J jnl
Halvade: scalable sequence analysis with MapReduce.
Bioinform.
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
2015 C conf
Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches.
WABI
Giles Miclotte, Mahdi Heydari, Piet Demeester, Pieter Audenaert, Jan Fostier
2015 — conf
Performance Analysis of a Parallel, Multi-node Pipeline for DNA Sequencing.
PPAM (2)
Dries Decap, Joke Reumers, Charlotte Herzeel, Pascal Costanza, Jan Fostier
2015 C conf
Towards Parallel Large-Scale Genomic Prediction by Coupling Sparse and Dense Matrix Algebra.
PDP
Arne De Coninck, Drosos Kourounis, Fabio Verbosio, Olaf Schenk, Bernard De Baets, Steven Maenhout, Jan Fostier
2014 J jnl
In-memory, distributed content-based recommender system.
J. Intell. Inf. Syst.
Simon Dooms, Pieter Audenaert, Jan Fostier, Toon De Pessemier, Luc Martens
2013 — conf
A Parallel, Distributed-Memory Framework for Comparative Motif Discovery.
PPAM (2)
Dieter De Witte, Michiel Van Bel, Pieter Audenaert, Piet Demeester, Bart Dhoedt, Klaas Vandepoele, Jan Fostier
2013 J jnl
EPSILON: an eQTL prioritization framework using similarity measures derived from local networks.
Bioinform.
Lieven P. C. Verbeke, Lore Cloots, Piet Demeester, Jan Fostier, Kathleen Marchal
2012 J jnl
Online execution time prediction for computationally intensive applications with periodic progress updates.
J. Supercomput.
Maria Chtepen, Filip H. A. Claeys, Bart Dhoedt, Filip De Turck, Jan Fostier, Piet Demeester, Peter A. Vanrolleghem
2011 J jnl
A greedy, graph-based algorithm for the alignment of multiple homologous gene lists.
Bioinform.
Jan Fostier, Sebastian Proost, Bart Dhoedt, Yvan Saeys, Piet Demeester, Yves Van de Peer, Klaas Vandepoele
2007 J jnl
A GRID Computer Implementation of the Multilevel Fast Multipole Algorithm for Full-Wave Analysis of Optical Devices.
IEICE Trans. Commun.
Jan Fostier, Femke Olyslager