Rayan Chikhi - Publications, H-index & Citations

Rayan Chikhi

pasteur institute

41H指数

163论文数

8.1K被引数

收录论文 33

发表时间

A versatile multi-components mixed model for bacterial-Genome Wide association studies 一种用于细菌全基因组关联研究的通用多组分混合模型

Nature Communications

IF15.7

2026-05-07

OAAI

Arthur Frouin; Fabien Laporte; Lukas Hafner; Mylène Maury; Zachary R. McCaw; Hanna Julienne; Léo Henches; Alexandre Leclercq; Rayan Chikhi; Marc Lecuit; Hugues Aschard

High-quality metagenome assembly from nanopore reads with nanoMDBG 使用nanoMDBG从纳米孔读长中组装高质量宏基因组

Nature Communications

IF15.7

2026-03-06

OAAI

Gaëtan Benoit; Robert James; Sébastien Raguideau; Georgina Alabone; Tim Goodall; Rayan Chikhi; Christopher Quince

Statistical signature of subtle behavioral changes in large-scale assays 大规模实验中细微行为变化的统计特征

plos biology

IF3.6

2025-04-21

OAAI

Blanc, Alexandre; Laurent, Francois; Barbier-Chebbah, Alex; Van Assel, Hugues; Cocanougher, Benjamin T.; Jones, Benjamin M. W.; Hague, Peter; Zlatic, Marta; Chikhi, Rayan; Vestergaard, Christian L.; Jovanic, Tihana; Masson, Jean-Baptiste; Barre, Chloe

Efficient and robust search of microbial genomes via phylogenetic compression 通过系统发育压缩实现微生物基因组的高效鲁棒搜索

NATURE METHODS

IF32.1

2025-04-09

OAAI

Brinda, Karel; Lima, Leandro; Pignotti, Simone; Quinones-Olvera, Natalia; Salikhov, Kamil; Chikhi, Rayan; Kucherov, Gregory

MUSET: set of utilities for constructing abundance unitig matrices from sequencing data MUSET：用于从测序数据构建丰度单元图矩阵的一组工具

BIOINFORMATICS

IF5.4

2025-02-03

OAAI

Vicedomini, Riccardo; Andreace, Francesco; Dufresne, Yoann; Chikhi, Rayan; Gonzalez, Camila Duitama

BFVD-a large repository of predicted viral protein structures

NUCLEIC ACIDS RESEARCH

IF13.1

2024-11-22

OAAI

Kim, Rachel Seongeun; Karin, Eli Levy; Mirdita, Milot; Chikhi, Rayan; Steinegger, Martin

Constructing and personalizing population pangenome graphs

NATURE METHODS

IF32.1

2024-10-21

PREAI

Chikhi, Rayan; Dufresne, Yoann; Medvedev, Paul

Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data Transipedia.org: 基于k-mer的大型RNA测序数据集的探索及其在癌症数据中的应用

GENOME BIOLOGY

IF9.4

2024-10-10

OAAI

Bessiere, Chloe; Xue, Haoliang; Guibert, Benoit; Boureux, Anthony; Ruffle, Florence; Viot, Julien; Chikhi, Rayan; Salson, Mikael; Marchet, Camille; Commes, Therese; Gautheret, Daniel

Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA

NATURE COMPUTATIONAL SCIENCE

IF18.3

2024-02-26

OAAI

Lemane, Teo; Lezzoche, Nolan; Lecubin, Julien; Pelletier, Eric; Lescot, Magali; Chikhi, Rayan; Peterlongo, Pierre

Petabase-Scale Homology Search for Structure Prediction

cold spring harbor perspectives in medicine

IF8.4

2024-02-05

PREAI

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

High-quality metagenome assembly from long accurate reads with metaMDBG 使用metaMDBG从长的准确读数中进行高质量的宏基因组组装

NATURE BIOTECHNOLOGY

IF41.7

2024-01-02

OAAI

Benoit, Gaetan; Raguideau, Sebastien; James, Robert; Phillippy, Adam M.; Chikhi, Rayan; Quince, Christopher

Comparing methods for constructing and representing human pangenome graphs 构建和表示人类pangenome图的方法比较

GENOME BIOLOGY

IF9.4

2023-11-30

OAAI

Andreace, Francesco; Lechat, Pierre; Dufresne, Yoann; Chikhi, Rayan

The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies

NATURE ECOLOGY & EVOLUTION

IF14.5

2023-11-06

OAAI

Willink, Beatriz; Tunstrom, Kalle; Nilen, Sofie; Chikhi, Rayan; Lemane, Teo; Takahashi, Michihiko; Takahashi, Yuma; Svensson, Erik I.; Wheat, Christopher West

Efficient mapping of accurate long reads in minimizer space with mapquik

GENOME RESEARCH

IF5.5

2023-06-30

OAAI

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

Hybrids of RNA viruses and viroid-like elements replicate in fungi RNA病毒和类病毒样元素的杂种在真菌中复制

NATURE COMMUNICATIONS

IF15.7

2023-05-05

OAAI

Forgia, Marco; Navarro, Beatriz; Daghino, Stefania; Cervera, Amelia; Gisel, Andreas; Perotto, Silvia; Aghayeva, Dilzara N.; Akinyuwa, Mary F.; Gobbi, Emanuela; Zheludev, Ivan N.; Edgar, Robert C.; Chikhi, Rayan; Turina, Massimo; Babaian, Artem; Di Serio, Francesco; de la Pena, Marcos

SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads SVDSS: 使用来自准确长读取的样本特定字符串在难以调用的基因组区域中发现结构变异

NATURE METHODS

IF32.1

2022-12-22

OAAI

Denti, Luca; Khorsand, Parsoa; Bonizzoni, Paola; Hormozdiari, Fereydoun; Chikhi, Rayan

Critical Assessment of Metagenome Interpretation: the second round of challenges

NATURE METHODS

IF32.1

2022-04-08

136

OAAI

Meyer, Fernando; Fritz, Adrian; Deng, Zhi-Luo; Koslicki, David; Lesker, Till Robin; Gurevich, Alexey; Robertson, Gary; Alser, Mohammed; Antipov, Dmitry; Beghini, Francesco; Bertrand, Denis; Brito, Jaqueline J.; Brown, C. Titus; Buchmann, Jan; Buluc, Aydin; Chen, Bo; Chikhi, Rayan; Clausen, Philip T. L. C.; Cristian, Alexandru; Dabrowski, Piotr Wojciech; Darling, Aaron E.; Egan, Rob; Eskin, Eleazar; Georganas, Evangelos; Goltsman, Eugene; Gray, Melissa A.; Hansen, Lars Hestbjerg; Hofmeyr, Steven; Huang, Pingqin; Irber, Luiz; Jia, Huijue; Jorgensen, Tue Sparholt; Kieser, Silas D.; Klemetsen, Terje; Kola, Axel; Kolmogorov, Mikhail; Korobeynikov, Anton; Kwan, Jason; LaPierre, Nathan; Lemaitre, Claire; Li, Chenhao; Limasset, Antoine; Malcher-Miranda, Fabio; Mangul, Serghei; Marcelino, Vanessa R.; Marchet, Camille; Marijon, Pierre; Meleshko, Dmitry; Mende, Daniel R.; Milanese, Alessio; Nagarajan, Niranjan; Nissen, Jakob; Nurk, Sergey; Oliker, Leonid; Paoli, Lucas; Peterlongo, Pierre; Piro, Vitor C.; Porter, Jacob S.; Rasmussen, Simon; Rees, Evan R.; Reinert, Knut; Renard, Bernhard; Robertsen, Espen Mikal; Rosen, Gail L.; Ruscheweyh, Hans-Joachim; Sarwal, Varuni; Segata, Nicola; Seiler, Enrico; Shi, Lizhen; Sun, Fengzhu; Sunagawa, Shinichi; Sorensen, Soren Johannes; Thomas, Ashleigh; Tong, Chengxuan; Trajkovski, Mirko; Tremblay, Julien; Uritskiy, Gherman; Vicedomini, Riccardo; Wang, Zhengyang; Wang, Ziye; Wang, Zhong; Warren, Andrew; Willassen, Nils Peder; Yelick, Katherine; You, Ronghui; Zeller, Georg; Zhao, Zhengqiao; Zhu, Shanfeng; Zhu, Jie; Garrido-Oter, Ruben; Gastmeier, Petra; Hacquard, Stephane; Haeussler, Susanne; Khaledi, Ariane; Maechler, Friederike; Mesny, Fantin; Radutoiu, Simona; Schulze-Lefert, Paul; Smit, Nathiana; Strowig, Till; Bremges, Andreas; Sczyrba, Alexander; McHardy, Alice Carolyn

Minimizer-space de Bruijn graphs: Whole-genome assembly of long reads in minutes on a personal computer

CELL SYSTEMS

IF7.7

2021-10-01

OAAI

Ekim, Baris; Berger, Bonnie; Chikhi, Rayan

Recombination Marks the Evolutionary Dynamics of a Recently Endogenized Retrovirus

MOLECULAR BIOLOGY AND EVOLUTION

IF5.3

2021-09-04

OAAI

Yang, Lei; Malhotra, Raunaq; Chikhi, Rayan; Elleder, Daniel; Kaiser, Theodora; Rong, Jesse; Medvedev, Paul; Poss, Mary

STRONG: metagenomics strain resolution on assembly graphs STRONG: 组装图上的宏基因组学菌株分辨率

GENOME BIOLOGY

IF9.4

2021-07-26

OAAI

Quince, Christopher; Nurk, Sergey; Raguideau, Sebastien; James, Robert; Soyer, Orkun S.; Summers, J. Kimberly; Limasset, Antoine; Eren, A. Murat; Chikhi, Rayan; Darling, Aaron E.

研究方向