84 entries « 1 of 5 »
1.

Cartes, Jorge Avila; Bonizzoni, Paola; Ciccolella, Simone; Vedova, Gianluca Della; Denti, Luca

PangeBlocks: customized construction of pangenome graphs via maximal blocks Journal Article

In: BMC Bioinformatics, vol. 25, no. 1, 2024, ISSN: 1471-2105.

Abstract | Links | BibTeX | Tags: WP2: Evolutionary/Comparative CPG

2.

Rizzo, Nicola; Equi, Massimo; Norri, Tuukka; Mäkinen, Veli

Elastic founder graphs improved and enhanced Journal Article

In: Theoretical Computer Science, vol. 982, no. 114269, pp. 114269, 2024, ISSN: 0304-3975.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

3.

Benoit, Gaëtan; Raguideau, Sébastien; James, Robert; Phillippy, Adam M.; Chikhi, Rayan; Quince, Christopher

High-quality metagenome assembly from long accurate reads with metaMDBG Journal Article

In: Nature Biotechnology, 2024, ISSN: 1546-1696.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

4.

Cartes, Jorge Avila; Bonizzoni, Paola; Ciccolella, Simone; Vedova, Gianluca Della; Denti, Luca; Didelot, Xavier; Monti, Davide Cesare; Pirola, Yuri

RecGraph: recombination-aware alignment of sequences to variation graphs Journal Article

In: Bioinformatics, vol. 40, no. 5, pp. btae292, 2024, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: WP2: Evolutionary/Comparative CPG

5.

Sauer, Lena M.; Cánovas, Rodrigo; Roche, Daniel Barry; Shams-Eldin, Hosam; Ravel, Patrice; Colinge, Jacques; Schwarz, Ralph T.; Mamoun, Choukri Ben; Rivals, Eric; Cornillot, Emmanuel

FT-GPI, a highly sensitive and accurate predictor of GPI-anchored proteins, reveals the composition and evolution of the GPI proteome in Plasmodium species Journal Article

In: Malaria Journal, vol. 22, no. 1, pp. 27-46, 2023, ISBN: 1475-2875.

Abstract | Links | BibTeX | Tags: Misc

6.

Kang, Xiongbin; Xu, Jialu; Luo, Xiao; Schönhuth, Alexander

Hybrid-hybrid correction of errors in long reads with HERO Journal Article

In: Genome Biol., vol. 24, no. 1, pp. 275, 2023, ISBN: 1474-760X.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

7.

Bernardini, Giulia; Fici, Gabriele; Gawrychowski, Paweł; Pissis, Solon P

Substring Complexity in Sublinear Space Proceedings Article

In: Iwata, Satoru; Kakimura, Naonori (Ed.): 34th International Symposium on Algorithms and Computation (ISAAC 2023), pp. 12:1–12:19, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2023, ISBN: 978-3-95977-289-1.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

8.

Loukides, Grigorios; Pissis, Solon P; Sweering, Michelle

Bidirectional string anchors for improved text indexing and top-$K$ similarity search Journal Article

In: IEEE Trans. Knowl. Data Eng., vol. 35, no. 11, pp. 11093–11111, 2023, ISBN: 1558-2191.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

9.

Romashchenko, Nikolai; Linard, Benjamin; Pardi, Fabio; Rivals, Eric

EPIK: Precise and scalable evolutionary placement with informative textitk-mers Journal Article

In: Bioinformatics, vol. 39, no. 12, 2023, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

10.

Andreace, Francesco; Lechat, Pierre; Dufresne, Yoann; Chikhi, Rayan

Comparing methods for constructing and representing human pangenome graphs Journal Article

In: Genome Biology, vol. 24, no. 1, pp. 274, 2023, ISSN: 1474-760X.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

11.

González, Camila Duitama; Rangavittal, Samarth; Vicedomini, Riccardo; Chikhi, Rayan; Richard, Hugues

aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets Journal Article

In: iScience, vol. 26, no. 11, pp. 108057, 2023, ISSN: 2589-0042.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

12.

Willink, Beatriz; Tunström, Kalle; Nilén, Sofie; Chikhi, Rayan; Lemane, Téo; Takahashi, Michihiko; Takahashi, Yuma; Svensson, Erik I.; Wheat, Christopher West

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies Journal Article

In: Nature Ecology & Evolution, vol. 8, no. 1, pp. 83–97, 2023, ISSN: 2397-334X.

Abstract | Links | BibTeX | Tags: WP2: Evolutionary/Comparative CPG, WP3: Translational CPG

13.

Herencsárová, Eva; Brejová, Broňa

Identifying Clusters in Graph Representations of Genomes Proceedings Article

In: Brejová, Broňa; Ciencialová, Lucie; Holeňa, Martin; Jajcay, Róbert; Jajcayová, Tatiana; Lexa, Matej; Mráz, František; Pardubská, Dana; Plátek, Martin (Ed.): Proceedings of the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), pp. 232–241, CEUR Workshop Proceedings, Tatranské Matliare, Slovakia, 2023.

Abstract | Links | BibTeX | Tags: WP2: Evolutionary/Comparative CPG

14.

Bernardini, Giulia; Iersel, Leo; Julien, Esther; Stougie, Leen

Constructing phylogenetic networks via cherry picking and machine learning Journal Article

In: Algorithms for Molecular Biology, vol. 18, no. 1, pp. 13, 2023, ISSN: 1748-7188.

Abstract | Links | BibTeX | Tags: WP2: Evolutionary/Comparative CPG

15.

Romashchenko, Nikolai; Linard, Benjamin; Rivals, Eric; Pardi, Fabio

Computing Phylo- k-mers Journal Article

In: IEEE/ACM Trans. Comput. Biol. Bioinform., vol. 20, no. 5, pp. 2889–2897, 2023, ISBN: 1557-9964.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

16.

Cozzi, Davide; Rossi, Massimiliano; Rubinacci, Simone; Gagie, Travis; Köppl, Dominik; Boucher, Christina; Bonizzoni, Paola

μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data Journal Article

In: Bioinformatics, vol. 39, no. 9, 2023, ISSN: 1367-4811.

Abstract | Links | BibTeX | Tags: WP2: Evolutionary/Comparative CPG

17.

Bonnet, Konstantinn; Marschall, Tobias; Doerr, Daniel

Constructing founder sets under allelic and non-allelic homologous recombination Journal Article

In: Algorithms Mol. Biol., vol. 18, no. 1, pp. 15, 2023, ISBN: 1748-7188.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

18.

Baláž, Andrej; Petescia, Alessia

Prefix-free graphs and suffix array construction in sublinear space Proceedings Article

In: Brejová, Broňa; Ciencialová, Lucie; Holeňa, Martin; Jajcay, Róbert; Jajcayová, Tatiana; Lexa, Matej; Mráz, František; Pardubská, Dana; Plátek, Martin (Ed.): Proceedings of the 23rd Conference Information Technologies – Applications and Theory (ITAT 2023), pp. 232–241, CEUR Workshop Proceedings, Tatranské Matliare, Slovakia, 2023.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

19.

Ayad, Lorraine A K; Chikhi, Rayan; Pissis, Solon P

Seedability: optimizing alignment parameters for sensitive sequence comparison Journal Article

In: Bioinform. Adv., vol. 3, no. 1, 2023, ISSN: 2635-0041.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG, WP2: Evolutionary/Comparative CPG

20.

Rizzo, Nicola; Cáceres, Manuel; Mäkinen, Veli

Finding Maximal Exact Matches in Graphs Proceedings Article

In: Belazzougui, Djamal; Ouangraoua, A"ida (Ed.): 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023), pp. 10:1–10:17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2023, ISBN: 978-3-95977-294-5.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG

84 entries « 1 of 5 »