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Year Number of Results
2010 1
2011 2
2012 3
2013 4
2014 4
2015 3
2016 4
2017 2
2018 3
2019 1
2020 5
2021 7
2022 8
2023 11
2024 5

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58 results

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Page 1
Petabase-scale sequence alignment catalyses viral discovery.
Edgar RC, Taylor B, Lin V, Altman T, Barbera P, Meleshko D, Lohr D, Novakovsky G, Buchfink B, Al-Shayeb B, Banfield JF, de la Peña M, Korobeynikov A, Chikhi R, Babaian A. Edgar RC, et al. Among authors: chikhi r. Nature. 2022 Feb;602(7895):142-147. doi: 10.1038/s41586-021-04332-2. Epub 2022 Jan 26. Nature. 2022. PMID: 35082445
Critical Assessment of Metagenome Interpretation: the second round of challenges.
Meyer F, Fritz A, Deng ZL, Koslicki D, Lesker TR, Gurevich A, Robertson G, Alser M, Antipov D, Beghini F, Bertrand D, Brito JJ, Brown CT, Buchmann J, Buluç A, Chen B, Chikhi R, Clausen PTLC, Cristian A, Dabrowski PW, Darling AE, Egan R, Eskin E, Georganas E, Goltsman E, Gray MA, Hansen LH, Hofmeyr S, Huang P, Irber L, Jia H, Jørgensen TS, Kieser SD, Klemetsen T, Kola A, Kolmogorov M, Korobeynikov A, Kwan J, LaPierre N, Lemaitre C, Li C, Limasset A, Malcher-Miranda F, Mangul S, Marcelino VR, Marchet C, Marijon P, Meleshko D, Mende DR, Milanese A, Nagarajan N, Nissen J, Nurk S, Oliker L, Paoli L, Peterlongo P, Piro VC, Porter JS, Rasmussen S, Rees ER, Reinert K, Renard B, Robertsen EM, Rosen GL, Ruscheweyh HJ, Sarwal V, Segata N, Seiler E, Shi L, Sun F, Sunagawa S, Sørensen SJ, Thomas A, Tong C, Trajkovski M, Tremblay J, Uritskiy G, Vicedomini R, Wang Z, Wang Z, Wang Z, Warren A, Willassen NP, Yelick K, You R, Zeller G, Zhao Z, Zhu S, Zhu J, Garrido-Oter R, Gastmeier P, Hacquard S, Häußler S, Khaledi A, Maechler F, Mesny F, Radutoiu S, Schulze-Lefert P, Smit N, Strowig T, Bremges A, Sczyrba A, McHardy AC. Meyer F, et al. Among authors: chikhi r. Nat Methods. 2022 Apr;19(4):429-440. doi: 10.1038/s41592-022-01431-4. Epub 2022 Apr 8. Nat Methods. 2022. PMID: 35396482 Free PMC article.
Disk compression of k-mer sets.
Rahman A, Chikhi R, Medvedev P. Rahman A, et al. Among authors: chikhi r. Algorithms Mol Biol. 2021 Jun 21;16(1):10. doi: 10.1186/s13015-021-00192-7. Algorithms Mol Biol. 2021. PMID: 34154632 Free PMC article.
Petascale Homology Search for Structure Prediction.
Lee S, Kim G, Karin EL, Mirdita M, Park S, Chikhi R, Babaian A, Kryshtafovych A, Steinegger M. Lee S, et al. Among authors: chikhi r. bioRxiv [Preprint]. 2023 Jul 11:2023.07.10.548308. doi: 10.1101/2023.07.10.548308. bioRxiv. 2023. PMID: 37503235 Free PMC article. Updated. Preprint.
Practical dynamic de Bruijn graphs.
Crawford VG, Kuhnle A, Boucher C, Chikhi R, Gagie T. Crawford VG, et al. Among authors: chikhi r. Bioinformatics. 2018 Dec 15;34(24):4189-4195. doi: 10.1093/bioinformatics/bty500. Bioinformatics. 2018. PMID: 29939217
Hybrids of RNA viruses and viroid-like elements replicate in fungi.
Forgia M, Navarro B, Daghino S, Cervera A, Gisel A, Perotto S, Aghayeva DN, Akinyuwa MF, Gobbi E, Zheludev IN, Edgar RC, Chikhi R, Turina M, Babaian A, Di Serio F, de la Peña M. Forgia M, et al. Among authors: chikhi r. Nat Commun. 2023 May 5;14(1):2591. doi: 10.1038/s41467-023-38301-2. Nat Commun. 2023. PMID: 37147358 Free PMC article.
STRONG: metagenomics strain resolution on assembly graphs.
Quince C, Nurk S, Raguideau S, James R, Soyer OS, Summers JK, Limasset A, Eren AM, Chikhi R, Darling AE. Quince C, et al. Among authors: chikhi r. Genome Biol. 2021 Jul 26;22(1):214. doi: 10.1186/s13059-021-02419-7. Genome Biol. 2021. PMID: 34311761 Free PMC article.
Petabase-Scale Homology Search for Structure Prediction.
Lee S, Kim G, Karin EL, Mirdita M, Park S, Chikhi R, Babaian A, Kryshtafovych A, Steinegger M. Lee S, et al. Among authors: chikhi r. Cold Spring Harb Perspect Biol. 2024 Feb 5:a041465. doi: 10.1101/cshperspect.a041465. Online ahead of print. Cold Spring Harb Perspect Biol. 2024. PMID: 38316555
58 results