77 entries « 1 of 4 »
1.

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

2.

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

3.

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

4.

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

5.

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

6.

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

7.

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

8.

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

9.

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

10.

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

11.

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

12.

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

13.

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

14.

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

15.

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

16.

Lee, Sewon; Kim, Gyuri; Karin, Eli Levy; Mirdita, Milot; Park, Sukhwan; Chikhi, Rayan; Babaian, Artem; Kryshtafovych, Andriy; Steinegger, Martin

Petascale Homology Search for Structure Prediction Unpublished

bioRxiv, 2023.

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

17.

Loukides, Grigorios; Pissis, Solon P.; Thankachan, Sharma V.; Zuba, Wiktor

Suffix-prefix queries on a dictionary Proceedings Article

In: Bulteau, Laurent; Lipt'ak, Zsuzsanna (Ed.): 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), pp. 21:1–21:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2023, ISBN: 978-3-95977-276-1.

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

18.

Gabory, Esteban; Mwaniki, Moses Njagi; Pisanti, Nadia; Pissis, Solon P; Radoszewski, Jakub; Sweering, Michelle; Zuba, Wiktor

Comparing elastic-degenerate strings: Algorithms, lower bounds, and applications Proceedings Article

In: Bulteau, Laurent; Lipt'ak, Zsuzsanna (Ed.): 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023), pp. 11:1–11:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2023, ISBN: 978-3-95977-276-1.

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

19.

Sládeček, Tomáš; Gažiová, Michaela; Kucharík, Marcel; Zaťková, Andrea; Pös, Zuzana; Pös, Ondrej; Krampl, Werner; Tomková, Erika; Hýblová, Michaela; Minárik, Gabriel; Radvánszky, Ján; Budiš, Jaroslav; Szemes, Tomáš

Combination of expert guidelines-based and machine learning-based approaches leads to superior accuracy of automated prediction of clinical effect of copy number variations Journal Article

In: Sci. Rep., vol. 13, no. 1, pp. 10531, 2023, ISBN: 2045-2322.

Abstract | Links | BibTeX | Tags: WP3: Translational CPG

20.

Ekim, Bariş; Sahlin, Kristoffer; Medvedev, Paul; Berger, Bonnie; Chikhi, Rayan

Efficient mapping of accurate long reads in minimizer space with mapquik Journal Article

In: Genome Research, 2023, ISSN: 1549-5469.

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

77 entries « 1 of 4 »