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Items: 22

1.

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

Heydari M, Miclotte G, Van de Peer Y, Fostier J.

BMC Bioinformatics. 2019 Jun 3;20(1):298. doi: 10.1186/s12859-019-2906-2.

2.

elPrep 4: A multithreaded framework for sequence analysis.

Herzeel C, Costanza P, Decap D, Fostier J, Verachtert W.

PLoS One. 2019 Feb 13;14(2):e0209523. doi: 10.1371/journal.pone.0209523. eCollection 2019.

3.

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

Vandersickel N, Watanabe M, Tao Q, Fostier J, Zeppenfeld K, Panfilov AV.

PLoS Comput Biol. 2018 Dec 20;14(12):e1006637. doi: 10.1371/journal.pcbi.1006637. eCollection 2018 Dec.

4.

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

Heydari M, Miclotte G, Van de Peer Y, Fostier J.

BMC Bioinformatics. 2018 Sep 4;19(1):311. doi: 10.1186/s12859-018-2319-7.

5.

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

Heydari M, Miclotte G, Demeester P, Van de Peer Y, Fostier J.

BMC Bioinformatics. 2017 Aug 18;18(1):374. doi: 10.1186/s12859-017-1784-8.

6.

OMSim: a simulator for optical map data.

Miclotte G, Plaisance S, Rombauts S, Van de Peer Y, Audenaert P, Fostier J.

Bioinformatics. 2017 Sep 1;33(17):2740-2742. doi: 10.1093/bioinformatics/btx293.

7.

Halvade-RNA: Parallel variant calling from transcriptomic data using MapReduce.

Decap D, Reumers J, Herzeel C, Costanza P, Fostier J.

PLoS One. 2017 Mar 30;12(3):e0174575. doi: 10.1371/journal.pone.0174575. eCollection 2017.

8.

Jabba: hybrid error correction for long sequencing reads.

Miclotte G, Heydari M, Demeester P, Rombauts S, Van de Peer Y, Audenaert P, Fostier J.

Algorithms Mol Biol. 2016 May 3;11:10. doi: 10.1186/s13015-016-0075-7. eCollection 2016.

9.

Needles: Toward Large-Scale Genomic Prediction with Marker-by-Environment Interaction.

De Coninck A, De Baets B, Kourounis D, Verbosio F, Schenk O, Maenhout S, Fostier J.

Genetics. 2016 May;203(1):543-55. doi: 10.1534/genetics.115.179887. Epub 2016 Mar 2.

10.

Efficient uncertainty quantification of large two-dimensional optical systems with a parallelized stochastic Galerkin method.

Zubac Z, Fostier J, De Zutter D, Vande Ginste D.

Opt Express. 2015 Nov 30;23(24):30833-50. doi: 10.1364/OE.23.030833.

PMID:
26698717
11.

INCLUDING EXPLICIT MARKER-BY-ENVIRONMENT INTERACTION FOR LARGE-SCALE GENOMIC PREDICTION.

De Coninck A, Kourounis D, Verbosio F, Schenk O, De Baets B, Maenhout S, Fostier J.

Commun Agric Appl Biol Sci. 2015;80(1):117-21. No abstract available.

PMID:
26630765
12.

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.

De Witte D, Van de Velde J, Decap D, Van Bel M, Audenaert P, Demeester P, Dhoedt B, Vandepoele K, Fostier J.

Bioinformatics. 2015 Dec 1;31(23):3758-66. doi: 10.1093/bioinformatics/btv466. Epub 2015 Aug 8.

13.

Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration.

Verbeke LP, Van den Eynden J, Fierro AC, Demeester P, Fostier J, Marchal K.

PLoS One. 2015 Jul 28;10(7):e0133503. doi: 10.1371/journal.pone.0133503. eCollection 2015.

14.

elPrep: High-Performance Preparation of Sequence Alignment/Map Files for Variant Calling.

Herzeel C, Costanza P, Decap D, Fostier J, Reumers J.

PLoS One. 2015 Jul 16;10(7):e0132868. doi: 10.1371/journal.pone.0132868. eCollection 2015.

15.

Frequency-based haplotype reconstruction from deep sequencing data of bacterial populations.

Pulido-Tamayo S, Sánchez-Rodríguez A, Swings T, Van den Bergh B, Dubey A, Steenackers H, Michiels J, Fostier J, Marchal K.

Nucleic Acids Res. 2015 Sep 18;43(16):e105. doi: 10.1093/nar/gkv478. Epub 2015 May 18.

16.

Halvade: scalable sequence analysis with MapReduce.

Decap D, Reumers J, Herzeel C, Costanza P, Fostier J.

Bioinformatics. 2015 Aug 1;31(15):2482-8. doi: 10.1093/bioinformatics/btv179. Epub 2015 Mar 26.

17.

DAIRRy-BLUP: a high-performance computing approach to genomic prediction.

De Coninck A, Fostier J, Maenhout S, De Baets B.

Genetics. 2014 Jul;197(3):813-22. doi: 10.1534/genetics.114.163683. Epub 2014 Apr 15.

18.

A high performance computing approach for genomic prediction.

De Coninck A, Fostier J, Maenhout S, De Baets B.

Commun Agric Appl Biol Sci. 2014;79(1):115-9. No abstract available.

PMID:
25864324
19.

The index-based subgraph matching algorithm (ISMA): fast subgraph enumeration in large networks using optimized search trees.

Demeyer S, Michoel T, Fostier J, Audenaert P, Pickavet M, Demeester P.

PLoS One. 2013 Apr 19;8(4):e61183. doi: 10.1371/journal.pone.0061183. Print 2013.

20.

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

Verbeke LP, Cloots L, Demeester P, Fostier J, Marchal K.

Bioinformatics. 2013 May 15;29(10):1308-16. doi: 10.1093/bioinformatics/btt142. Epub 2013 Apr 16.

PMID:
23595663
21.

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.

Proost S, Fostier J, De Witte D, Dhoedt B, Demeester P, Van de Peer Y, Vandepoele K.

Nucleic Acids Res. 2012 Jan;40(2):e11. doi: 10.1093/nar/gkr955. Epub 2011 Nov 18.

22.

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

Fostier J, Proost S, Dhoedt B, Saeys Y, Demeester P, Van de Peer Y, Vandepoele K.

Bioinformatics. 2011 Mar 15;27(6):749-56. doi: 10.1093/bioinformatics/btr008. Epub 2011 Jan 6.

PMID:
21216775

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