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)

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)

O(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)

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)

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 (PPAM (2), 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)

In-memory, distributed content-based recommender system. - Simon Dooms; Pieter Audenaert; Jan Fostier; Toon De Pessemier; Luc Martens (J. Intell. Inf. Syst., 2014)

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 (PDP, 2015)

Performance Analysis of a Parallel, Multi-node Pipeline for DNA Sequencing. - Dries Decap; Joke Reumers; Charlotte Herzeel; Pascal Costanza; Jan Fostier (PPAM (2), 2015)

Jabba: Hybrid Error Correction for Long Sequencing Reads Using Maximal Exact Matches. - Giles Miclotte; Mahdi Heydari; Piet Demeester; Pieter Audenaert; Jan Fostier (WABI, 2015)

Halvade: scalable sequence analysis with MapReduce. - Dries Decap; Joke Reumers; Charlotte Herzeel; Pascal Costanza; Jan Fostier (Bioinform., 2015)

BLSSpeller: exhaustive comparative discovery of conserved cis-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)

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)

OMSim: a simulator for optical map data. - Giles Miclotte; Stéphane Plaisance; Stephane Rombauts; Yves Van de Peer; Pieter Audenaert; Jan Fostier (Bioinform., 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)

A BLAS-Based Algorithm for Finding Position Weight Matrix Occurrences in DNA Sequences on CPUs and GPUs. - Jan Fostier (IWBBIO (1), 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)

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)

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)

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)

Accurate determination of node and arc multiplicities in de bruijn graphs using conditional random fields. - Aranka Steyaert; Pieter Audenaert; Jan Fostier (BMC Bioinform., 2020)

Approximate Pattern Matching Using Search Schemes and In-Text Verification. - Luca Renders; Lore Depuydt; Jan Fostier (IWBBIO (2), 2022)

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 (EUSIPCO, 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)

Pan-genome de Bruijn graph using the bidirectional FM-index. - Lore Depuydt; Luca Renders; Thomas Abeel; Jan Fostier (BMC Bioinform., 2023)

Faster Maximal Exact Matches with Lazy LCP Evaluation. - Adrián Goga; Lore Depuydt; Nathaniel K. Brown; Jan Fostier; Travis Gagie; Gonzalo Navarro 001 (DCC, 2024)

Automated Design of Efficient Search Schemes for Lossless Approximate Pattern Matching. - Luca Renders; Lore Depuydt; Sven Rahmann; Jan Fostier (RECOMB, 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 (WABI, 2024)

Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes. - Luca Renders; Lore Depuydt; Sven Rahmann; Jan Fostier (J. Comput. Biol., 2024)

Search Schemes for Approximate Pattern Matching: An Overview. - Lore Depuydt; Jan Fostier; Simon Gottlieb; Gregory Kucherov; Knut Reinert; Luca Renders (The Expanding World of Compressed Data, 2025)

b-move: faster lossless approximate pattern matching in a run-length compressed index. - Lore Depuydt; Luca Renders; Simon Van de Vyver; Lennart Veys; Travis Gagie; Jan Fostier (Algorithms Mol. Biol., 2025)