37 entries « 1 of 2 »
1.

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

2.

Mwaniki, Njagi Moses; Pisanti, Nadia

Optimal Sequence Alignment to ED-Strings Proceedings Article

In: Bansal, Mukul S.; Cai, Zhipeng; Mangul, Serghei (Ed.): Bioinformatics Research and Applications, pp. 204–216, Springer Nature, Germany, 2023, ISSN: 0302-9743.

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

3.

Blassel, Luc; Medvedev, Paul; Chikhi, Rayan

Mapping-friendly sequence reductions: Going beyond homopolymer compression Journal Article

In: iScience, vol. 25, no. 11, pp. 105305, 2022, ISSN: 2589-0042.

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

4.

Luo, Xiao; Kang, Xiongbin; Schönhuth, Alexander

VeChat: correcting errors in long reads using variation graphs Journal Article

In: Nat Commun, vol. 13, no. 1, pp. 6657, 2022, ISSN: 2041-1723.

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

5.

Lemane, Téo; Chikhi, Rayan; Peterlongo, Pierre

kmdiff, large-scale and user-friendly differential k-mer analyses Journal Article

In: Bioinformatics, vol. 38, no. 24, pp. 5443-5445, 2022, ISSN: 1367-4803.

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

6.

Dufresne, Yoann; Lemane, Teo; Marijon, Pierre; Peterlongo, Pierre; Rahman, Amatur; Kokot, Marek; Medvedev, Paul; Deorowicz, Sebastian; Chikhi, Rayan

The K-mer File Format: a standardized and compact disk representation of sets of k-mers Journal Article

In: Bioinformatics, vol. 38, no. 18, pp. 4423–4425, 2022, ISSN: 1367-4811.

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

7.

Kang, Xiongbin; Luo, Xiao; Schönhuth, Alexander

StrainXpress: strain aware metagenome assembly from short reads Journal Article

In: Nucleic Acids Res, vol. 50, no. 17, pp. e101, 2022, ISSN: 1362-4962.

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

8.

Charalampopoulos, Panagiotis; Pissis, Solon P.; Radoszewski, Jakub

Longest Palindromic Substring in Sublinear Time Proceedings Article

In: Bannai, Hideo; Holub, Jan (Ed.): 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), pp. 20:1–20:9, Schloss Dagstuhl -- Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2022, ISSN: 1868-8969.

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

9.

Bernardini, Giulia; Conte, Alessio; Gabory, Esteban; Grossi, Roberto; Loukides, Grigorios; Pissis, Solon P.; Punzi, Giulia; Sweering, Michelle

On Strings Having the Same Length- k Substrings Proceedings Article

In: Bannai, Hideo; Holub, Jan (Ed.): 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), pp. 16:1–16:17, Schloss Dagstuhl -- Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2022, ISSN: 1868-8969.

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

10.

Teramo, Antonella; Binatti, Andrea; Ciabatti, Elena; Schiavoni, Gianluca; Tarrini, Giulia; Baril`a, Gregorio; Calabretto, Giulia; Vicenzetto, Cristina; Gasparini, Vanessa Rebecca; Facco, Monica; Petrini, Iacopo; Grossi, Roberto; Pisanti, Nadia; Bortoluzzi, Stefania; Falini, Brunangelo; Tiacci, Enrico; Galimberti, Sara; Semenzato, Gianpietro; Zambello, Renato

Defining TCRγδlymphoproliferative disorders by combined immunophenotypic and molecular evaluation Journal Article

In: Nature Communications, vol. 13, no. 1, pp. 3298, 2022, ISBN: 2041-1723.

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

11.

Bernardini, Giulia; Chen, Huiping; Loukides, Grigorios; Pissis, Solon P.; Stougie, Leen; Sweering, Michelle

Making de Bruijn Graphs Eulerian Proceedings Article

In: Bannai, Hideo; Holub, Jan (Ed.): 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022), pp. 12:1–12:18, Schloss Dagstuhl -- Leibniz-Zentrum für Informatik, Dagstuhl, Germany, 2022, ISSN: 1868-8969.

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

12.

Sládeček, T.; Gažiová, M.; Pös, O.; Pös, Z.; Budiš, J.; Radvánsky, J.; Szemes, T.

Combination of expert decision systems with artificial intelligence leads to superior accuracy of automated prediction of clinical effect of copy number variation Presentation

Poster Presentation at ESHG, 01.06.2022.

BibTeX | Tags: Misc, WP3: Translational CPG

13.

Bernardini, Giulia; Gawrychowski, Paweł; Pisanti, Nadia; Pissis, Solon P.; Rosone, Giovanna

Elastic-Degenerate String Matching via Fast Matrix Multiplication Journal Article

In: SIAM Journal on Computing, vol. 51, no. 3, pp. 549–576, 2022.

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

14.

Charalampopoulos, Panagiotis; Iliopoulos, Costas S.; Kociumaka, Tomasz; Pissis, Solon P.; Radoszewski, Jakub; Straszy'nski, Juliusz

Efficient Computation of Sequence Mappability Journal Article

In: Algorithmica, vol. 84, no. 5, pp. 1418–1440, 2022, ISBN: 1432-0541.

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

15.

Baaijens, Jasmijn A.; Bonizzoni, Paola; Boucher, Christina; Vedova, Gianluca Della; Pirola, Yuri; Rizzi, Raffaella; Sirén, Jouni

Computational graph pangenomics: a tutorial on data structures and their applications Journal Article

In: Natural Computing, vol. 21, no. 1, pp. 81–108, 2022, ISBN: 1572-9796.

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

16.

Luo, Xiao; Kang, Xiongbin; Schönhuth, Alexander

Strainline: full-length de novo viral haplotype reconstruction from noisy long reads Journal Article

In: Genome Biology, vol. 23, iss. 1, no. 29, pp. 1–27, 2022, ISSN: 1474-760X.

Abstract | Links | BibTeX | Tags: WP1: Primary CPG, WP3: Translational CPG

17.

Gažiová, M.; Sládeček, T.; Pös, O.; Števko, M.; Krampl, W.; Pös, Z.; Hekel, R.; Hlavačka, M.; Kucharík, M.; Radvánszky, J.; Budiš, J.; Szemes, T.

Automated prediction of the clinical impact of structural copy number variations Journal Article

In: Scientific Reports, vol. 12, no. 1, pp. 555, 2022, ISSN: 2045-2322.

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

18.

Rizzo, Nicola; Mäkinen, Veli

Linear Time Construction of Indexable Elastic Founder Graphs Proceedings Article

In: Bazgan, Cristina; Fernau, Henning (Ed.): Combinatorial Algorithms, pp. 480–493, Springer International Publishing, Cham, 2022, ISBN: 978-3-031-06678-8.

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

19.

Mwaniki, Njagi Moses; Garrison, Erik; Pisanti, Nadia

Fast Exact String to D-Texts Alignments Unpublished

arXiv, 2022.

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

20.

Zhong, Haodi; Loukides, Grigorios; Pissis, Solon P.

Clustering sequence graphs Journal Article

In: Data & Knowledge Engineering, vol. 138, pp. 101981, 2022, ISSN: 0169-023X.

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

37 entries « 1 of 2 »