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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: yelick k. 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.
Terabase-Scale Coassembly of a Tropical Soil Microbiome.
Riley R, Bowers RM, Camargo AP, Campbell A, Egan R, Eloe-Fadrosh EA, Foster B, Hofmeyr S, Huntemann M, Kellom M, Kimbrel JA, Oliker L, Yelick K, Pett-Ridge J, Salamov A, Varghese NJ, Clum A. Riley R, et al. Among authors: yelick k. Microbiol Spectr. 2023 Aug 17;11(4):e0020023. doi: 10.1128/spectrum.00200-23. Epub 2023 Jun 13. Microbiol Spectr. 2023. PMID: 37310219 Free PMC article.
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: yelick k. Sci Rep. 2020 Jul 1;10(1):10689. doi: 10.1038/s41598-020-67416-5. Sci Rep. 2020. PMID: 32612216 Free PMC article.
Exascale applications: skin in the game.
Alexander F, Almgren A, Bell J, Bhattacharjee A, Chen J, Colella P, Daniel D, DeSlippe J, Diachin L, Draeger E, Dubey A, Dunning T, Evans T, Foster I, Francois M, Germann T, Gordon M, Habib S, Halappanavar M, Hamilton S, Hart W, Henry Huang Z, Hungerford A, Kasen D, Kent PRC, Kolev T, Kothe DB, Kronfeld A, Luo Y, Mackenzie P, McCallen D, Messer B, Mniszewski S, Oehmen C, Perazzo A, Perez D, Richards D, Rider WJ, Rieben R, Roche K, Siegel A, Sprague M, Steefel C, Stevens R, Syamlal M, Taylor M, Turner J, Vay JL, Voter AF, Windus TL, Yelick K. Alexander F, et al. Among authors: yelick k. Philos Trans A Math Phys Eng Sci. 2020 Mar 6;378(2166):20190056. doi: 10.1098/rsta.2019.0056. Epub 2020 Jan 20. Philos Trans A Math Phys Eng Sci. 2020. PMID: 31955678 Free PMC article.
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. 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.
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: yelick ka. Genome Biol. 2015 Jan 31;16(1):26. doi: 10.1186/s13059-015-0582-8. Genome Biol. 2015. PMID: 25637298 Free PMC article.
MRI measures of fat infiltration in the lower extremities following motor incomplete spinal cord injury: reliability and potential implications for muscle activation.
Smith AC, Knikou M, Yelick KL, Alexander AR, Murnane MM, Kritselis AA, Houmpavlis PJ, McPherson JG, Wasielewski M, Hoggarth MA, Elliott JM. Smith AC, et al. Among authors: yelick kl. Annu Int Conf IEEE Eng Med Biol Soc. 2016 Aug;2016:5451-5456. doi: 10.1109/EMBC.2016.7591960. Annu Int Conf IEEE Eng Med Biol Soc. 2016. PMID: 28269491