MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes
Peer Community Journal Néron B, Denise R, Coluzzi C, Touchon M, Rocha EP, Abby SS. Complex cellular functions are usually encoded by a...
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Feb 27, 2023
Yersiniomics, a Multi-Omics Interactive Database for Yersinia Species.
Microbiol Spectr. Lê-Bury P, Druart K, Savin C, Lechat P, Mas Fiol G, Matondo M, Bécavin C, Dussurget O, Pizarro-Cerdá J. The genus...
Jan 7, 2023
Deep learning in image-based phenotypic drug discovery.
Trends Cell Biol. Krentzel D, Shorte SL, Zimmer C. Modern drug discovery approaches often use high-content imaging to systematically...
Dec 22, 2022
SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings
Full title: SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads...
Dec 15, 2022
large-scale and user-friendly differential k-mer analyses
Bioinformatics Téo Lemane, Rayan Chikhi, Pierre Peterlongo Genome wide association studies elucidate links between genotypes and ...
Nov 18, 2022
Mapping-friendly sequence reductions: going beyond homopolymer compression
iScience Blassel, P. Medvedev, R. Chikhi Sequencing errors continue to pose algorithmic challenges to methods working with sequencing...
Oct 17, 2022
Smart Learning of Click and Refine for Nuclei Segmentation on Histology Images
2022 IEEE International Conference on Image Processing Habis, V. Meas-Yedid, D. F. González Obando, J. -C. Olivo-Marin and E. D. Angelini...
Sep 17, 2022
The K-mer File Format: a standardized and compact disk representation of sets of k-mers.
Bioinformatics Dufresne Y, Lemane T, Marijon P, Peterlongo P, Rahman A, Kokot M, Medvedev P, Deorowicz S, Chikhi R. Sets of k-mers are...
Apr 28, 2022
kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections
Bioinformatics Advances Téo Lemane, Paul Medvedev, Rayan Chikhi, Pierre Peterlongo When indexing large collections of short-read...
Apr 12, 2022
4th Workshop Single-Cell 2022 - Single-Cell : Transcriptomics, Spatial and Multi-Omics (sincellTE)
Date: From 01/09/2022 to 01/14/2022 Place: Station Biologique, Roscoff, France This workshop focuses on the large-scale study of...
Mar 24, 2022
IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria
Full title: IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in...
Jan 31, 2022
New Approach to Accelerated Image Annotation by Leveraging Virtual Reality and Cloud Computing.
Front Bioinform Guérinot C, Marcon V, Godard C, Blanc T, Verdier H, Planchon G, Raimondi F, Boddaert N, Alonso M, Sailor K, Lledo PM,...
Jan 26, 2022
Petabase-scale sequence alignment catalyses viral discovery
Nature Edgar, R.C., Taylor, J., Lin, V. et al Public databases contain a planetary collection of nucleic acid sequences, but their...
Jan 22, 2022
Towards Human in the Loop Analysis of Complex Point Clouds
Full title: Towards Human in the Loop Analysis of Complex Point Clouds: Advanced Visualizations, Quantifications, and Communication...
Jul 14, 2021
Quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
Published in Bioinformatics Mallet V, Nilges M, Bouvier G Summary: We implemented the Self-Organizing Maps algorithm running efficiently...
May 30, 2021
Comparative genome analysis using sample-specific string detection in accurate long reads
Parsoa Khorsand, Luca Denti, Human Genome Structural Variant Consortium, Paola Bonizzoni, Rayan Chikhi, Fereydoun Hormozdiari...
Mar 31, 2021
Data Structures to Represent a Set of k-long DNA Sequences
ACM Computing Surveys Chikhi R, Holub J, Medvedev P The analysis of biological sequencing data has been one of the biggest applications...
Dec 1, 2020
Data structures based on kmers for querying large collections of sequencing data sets
Genome Res Marchet C, Boucher C, Puglisi SJ, Medvedev P, Salson M, Chikhi R High-throughput sequencing data sets are usually deposited...
Nov 23, 2020
Identifying neural substrates of competitive interactions and sequence transitions
Plos Genetics Jean-Baptiste Masson, Francois Laurent, Albert Cardona, Chloe Barre, Nicolas Skatchkovsky, Marta Zlatic, Tihana Jovanic...
Sep 6, 2020
Disk Compression of k-mer Sets
WABI Rahman A, Chikhi R, Medvedev P K-mer based methods have become prevalent in many areas of bioinformatics. In applications such as...
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