Author details

Full Name

Rayan Chikhi

Affiliation

ORCID

Career Start Year

2010

Papers

H Index

Expertise

CM4AI Collaborator

PMID	Paper Title	Journal Title	Published Year
37503235	Petascale Homology Search for Structure Prediction.	bioRxiv	2023
38037131	Comparing methods for constructing and representing human pangenome graphs.		2023
37932383	The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.		2023
37926832	decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.		2023
37876815	aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.		2023
37786716	Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs.	bioRxiv	2023
37621456	Seedability: optimizing alignment parameters for sensitive sequence comparison.		2023
37399256	Efficient mapping of accurate long reads in minimizer space with mapquik.	Genome Res	2023
37147358	Hybrids of RNA viruses and viroid-like elements replicate in fungi.		2023
37131636	Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression.		2023
36550274	SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads.	Nat Methods	2023
35082445	Petabase-scale sequence alignment catalyses viral discovery.	Nature	2022
36315078	k mdiff, large-scale and user-friendly differential k-mer analyses.		2022
36111873	Draft genome of the lowland anoa (Bubalus depressicornis) and comparison with buffalo genome assemblies (Bovidae, Bubalina).	G3: Genes, Genomes, Genetics	2022
35904548	The K-mer File Format: a standardized and compact disk representation of sets of k-mers.		2022
36339268	Mapping-friendly sequence reductions: Going beyond homopolymer compression.	iScience	2022
36699393	kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections.		2022
34525345	Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer.	Cell Syst	2021
36700094	Comparative genome analysis using sample-specific string detection in accurate long reads.	Bioinform Adv	2021
34154632	Disk compression of k-mer sets.	Algorithms for Molecular Biology	2021
34311761	STRONG: metagenomics strain resolution on assembly graphs.		2021
34301928	Strainberry: automated strain separation in low-complexity metagenomes using long reads.	Nature Communications	2021
33328168	Data structures based on -mers for querying large collections of sequencing data sets.	Genome Research	2021
34480565	Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus.	Mol Biol Evol	2021
31232449	Comparative assessment of long-read error correction software applied to Nanopore RNA-sequencing data.	Briefings in Bioinformatics	2020
32315402	yacrd and fpa: upstream tools for long-read genome assembly.		2020
31806764	Genome Assembly and Analysis of the North American Mountain Goat () Reveals Species-Level Responses to Extreme Environments.	G3: Genes, Genomes, Genetics	2020
32657392	REINDEER: efficient indexing of k-mer presence and abundance in sequencing datasets.		2020
30918948	Graph analysis of fragmented long-read bacterial genome assemblies.		2019
29194476	RecoverY: k-mer-based read classification for Y-chromosome-specific sequencing and assembly.		2018
29939217	Practical dynamic de Bruijn graphs.		2018
29620920	AllSome Sequence Bloom Trees.	Journal of Computational Biology	2018
29284518	DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition.		2017
28967888	Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.	Nat Methods	2017
27307618	Compacting de Bruijn graphs from sequencing data quickly and in low memory.		2016
27153683	Assembly scaffolding with PE-contaminated mate-pair libraries.		2016
26934921	A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y.	Genome Research	2016
27187213	Giraffe genome sequence reveals clues to its unique morphology and physiology.	Nat Commun	2016
25404127	Reference-free detection of isolated SNPs.	Nucleic Acids Research	2015
25629448	On the representation of de Bruijn graphs.	J Comput Biol	2015
25123898	MindTheGap: integrated detection and assembly of short and long insertions.		2014
23732276	Informed and automated k-mer size selection for genome assembly.		2014
24990603	GATB: Genome Assembly & Analysis Tool Box.		2014
23325618	DSK: k-mer counting with very low memory usage.		2013
23870653	Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.	Gigascience	2013
24040893	Space-efficient and exact de Bruijn graph representation based on a Bloom filter.	Algorithms for Molecular Biology	2013
23282463	Compareads: comparing huge metagenomic experiments.	BMC Bioinformatics	2012
22537044	KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.	BMC Bioinformatics	2012
22443449	Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.	BMC Bioinformatics	2012
21787306	Molecular surface representation using 3D Zernike descriptors for protein shape comparison and docking.	Curr Protein Pept Sci	2011