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The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals.
Schnitzler CE, Chang ES, Waletich J, Quiroga-Artigas G, Wong WY, Nguyen AD, Barreira SN, Doonan LB, Gonzalez P, Koren S, Gahan JM, Sanders SM, Bradshaw B, DuBuc TQ, Febrimarsa, de Jong D, Nawrocki EP, Larson A, Klasfeld S, Gornik SG, Moreland RT, Wolfsberg TG, Phillippy AM, Mullikin JC, Simakov O, Cartwright P, Nicotra M, Frank U, Baxevanis AD. Schnitzler CE, et al. Among authors: phillippy am. Genome Res. 2024 Apr 25;34(3):498-513. doi: 10.1101/gr.278382.123. Genome Res. 2024. PMID: 38508693 Free PMC article.
Epigenetic control and inheritance of rDNA arrays.
Potapova T, Kostos P, McKinney S, Borchers M, Haug J, Guarracino A, Solar S, Gogol M, Monfort Anez G, de Lima LG, Wang Y, Hall K, Hoffman S, Garrison E, Phillippy AM, Gerton JL. Potapova T, et al. Among authors: phillippy am. bioRxiv [Preprint]. 2024 Sep 16:2024.09.13.612795. doi: 10.1101/2024.09.13.612795. bioRxiv. 2024. PMID: 39372739 Free PMC article. Preprint.
High-quality metagenome assembly from long accurate reads with metaMDBG.
Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, Quince C. Benoit G, et al. Among authors: phillippy am. Nat Biotechnol. 2024 Sep;42(9):1378-1383. doi: 10.1038/s41587-023-01983-6. Epub 2024 Jan 2. Nat Biotechnol. 2024. PMID: 38168989 Free PMC article.
Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y; Human Pangenome Reference Consortium; Marschall T, Li H, Paten B. Hickey G, et al. Nat Biotechnol. 2024 Apr;42(4):663-673. doi: 10.1038/s41587-023-01793-w. Epub 2023 May 10. Nat Biotechnol. 2024. PMID: 37165083 Free PMC article.
Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.
Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Jain N, Johnson C, Kim H, Lee C, Marques-Bonet T, O'Toole B, Rhie A, Secomandi S, Sozzoni M, Tilley T, Uliano-Silva M, van den Beek M, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G. Larivière D, et al. Among authors: phillippy am. bioRxiv [Preprint]. 2023 Jun 30:2023.06.28.546576. doi: 10.1101/2023.06.28.546576. bioRxiv. 2023. Update in: Nat Biotechnol. 2024 Mar;42(3):367-370. doi: 10.1038/s41587-023-02100-3 PMID: 37425881 Free PMC article. Updated. Preprint.
152 results