Pierre Peterlongo
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Explore the profile of Pierre Peterlongo including associated specialties, affiliations and a list of published articles.
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37
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934
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Recent Articles
1.
Levallois V, Andreace F, Le Gal B, Dufresne Y, Peterlongo P
iScience
. 2024 Dec;
27(12):111435.
PMID: 39720533
Genomic data sequencing is crucial for understanding biological systems. As genomic databases like the European Nucleotide Archive expand exponentially, efficient data manipulation is essential. A key challenge is querying these...
2.
Lemane T, Lezzoche N, Lecubin J, Pelletier E, Lescot M, Chikhi R, et al.
Nat Comput Sci
. 2024 Feb;
4(2):104-109.
PMID: 38413777
Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex,...
3.
Robidou L, Peterlongo P
Bioinformatics
. 2023 May;
39(5).
PMID: 37195454
Motivation: High throughput sequencing technologies generate massive amounts of biological sequence datasets as costs fall. One of the current algorithmic challenges for exploiting these data on a global scale consists...
4.
Kirsch-Gerweck B, Bohnenkamper L, Henrichs M, Alanko J, Bannai H, Cazaux B, et al.
Mol Biol Evol
. 2023 Feb;
40(3).
PMID: 36790822
Genomic regions under positive selection harbor variation linked for example to adaptation. Most tools for detecting positively selected variants have computational resource requirements rendering them impractical on population genomic datasets...
5.
kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections
Lemane T, Medvedev P, Chikhi R, Peterlongo P
Bioinform Adv
. 2023 Jan;
2(1):vbac029.
PMID: 36699393
Summary: When indexing large collections of short-read sequencing data, a common operation that has now been implemented in several tools (Sequence Bloom Trees and variants, BIGSI) is to construct a...
6.
Lemane T, Chikhi R, Peterlongo P
Bioinformatics
. 2022 Oct;
38(24):5443-5445.
PMID: 36315078
Summary: Genome wide association studies elucidate links between genotypes and phenotypes. Recent studies point out the interest of conducting such experiments using k-mers as the base signal instead of single-nucleotide...
7.
Richter D, Watteaux R, Vannier T, Leconte J, Fremont P, Reygondeau G, et al.
Elife
. 2022 Aug;
11.
PMID: 35920817
Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated....
8.
Dufresne Y, Lemane T, Marijon P, Peterlongo P, Rahman A, Kokot M, et al.
Bioinformatics
. 2022 Jul;
38(18):4423-4425.
PMID: 35904548
Summary: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a...
9.
Meyer F, Fritz A, Deng Z, Koslicki D, Lesker T, Gurevich A, et al.
Nat Methods
. 2022 Apr;
19(4):429-440.
PMID: 35396482
Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to...
10.
Da Silva K, Pons N, Berland M, Plaza Onate F, Almeida M, Peterlongo P
PeerJ
. 2021 Sep;
9:e11884.
PMID: 34513324
Current studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances...