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Critical Assessment of Metagenome Interpretation: the second round of challenges.
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.
A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome.
Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS.
Chapman JA, et al. Among authors: buluc a.
Genome Biol. 2015 Jan 31;16(1):26. doi: 10.1186/s13059-015-0582-8.
Genome Biol. 2015.
PMID: 25637298
Free PMC article.
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The parallelism motifs of genomic data analysis.
Yelick K, Buluç A, Awan M, Azad A, Brock B, Egan R, Ekanayake S, Ellis M, Georganas E, Guidi G, Hofmeyr S, Selvitopi O, Teodoropol C, Oliker L.
Yelick K, et al. Among authors: buluc a.
Philos Trans A Math Phys Eng Sci. 2020 Mar 6;378(2166):20190394. doi: 10.1098/rsta.2019.0394. Epub 2020 Jan 20.
Philos Trans A Math Phys Eng Sci. 2020.
PMID: 31955674
Free PMC article.
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Terabase-scale metagenome coassembly with MetaHipMer.
Hofmeyr S, Egan R, Georganas E, Copeland AC, Riley R, Clum A, Eloe-Fadrosh E, Roux S, Goltsman E, Buluç A, Rokhsar D, Oliker L, Yelick K.
Hofmeyr S, et al. Among authors: buluc a.
Sci Rep. 2020 Jul 1;10(1):10689. doi: 10.1038/s41598-020-67416-5.
Sci Rep. 2020.
PMID: 32612216
Free PMC article.
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ADEPT: a domain independent sequence alignment strategy for gpu architectures.
Awan MG, Deslippe J, Buluc A, Selvitopi O, Hofmeyr S, Oliker L, Yelick K.
Awan MG, et al. Among authors: buluc a.
BMC Bioinformatics. 2020 Sep 15;21(1):406. doi: 10.1186/s12859-020-03720-1.
BMC Bioinformatics. 2020.
PMID: 32933482
Free PMC article.
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Unraveling the functional dark matter through global metagenomics.
Pavlopoulos GA, Baltoumas FA, Liu S, Selvitopi O, Camargo AP, Nayfach S, Azad A, Roux S, Call L, Ivanova NN, Chen IM, Paez-Espino D, Karatzas E; Novel Metagenome Protein Families Consortium; Iliopoulos I, Konstantinidis K, Tiedje JM, Pett-Ridge J, Baker D, Visel A, Ouzounis CA, Ovchinnikov S, Buluç A, Kyrpides NC.
Pavlopoulos GA, et al. Among authors: buluc a.
Nature. 2023 Oct;622(7983):594-602. doi: 10.1038/s41586-023-06583-7. Epub 2023 Oct 11.
Nature. 2023.
PMID: 37821698
Free PMC article.
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HipMCL: a high-performance parallel implementation of the Markov clustering algorithm for large-scale networks.
Azad A, Pavlopoulos GA, Ouzounis CA, Kyrpides NC, Buluç A.
Azad A, et al. Among authors: buluc a.
Nucleic Acids Res. 2018 Apr 6;46(6):e33. doi: 10.1093/nar/gkx1313.
Nucleic Acids Res. 2018.
PMID: 29315405
Free PMC article.
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Fast intratumor heterogeneity inference from single-cell sequencing data.
Kızılkale C, Rashidi Mehrabadi F, Sadeqi Azer E, Pérez-Guijarro E, Marie KL, Lee MP, Day CP, Merlino G, Ergün F, Buluç A, Sahinalp SC, Malikić S.
Kızılkale C, et al. Among authors: buluc a.
Nat Comput Sci. 2022 Sep;2(9):577-583. doi: 10.1038/s43588-022-00298-x. Epub 2022 Sep 8.
Nat Comput Sci. 2022.
PMID: 38177468
Free PMC article.
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