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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, Antunes A, Balacco JR, Chaisson MJP, Cheng H, Collins J, Couture M, Denisova A, Fedrigo O, Gallo GR, Giani AM, Gooder GM, Horan K, 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, Williams RW, Waterhouse RM, Phillippy AM, Jarvis ED, Schatz MC, Nekrutenko A, Formenti G. Larivière D, et al. Among authors: antunes a. Nat Biotechnol. 2024 Mar;42(3):367-370. doi: 10.1038/s41587-023-02100-3. Nat Biotechnol. 2024. PMID: 38278971 No abstract available.
Bone-associated gene evolution and the origin of flight in birds.
Machado JP, Johnson WE, Gilbert MT, Zhang G, Jarvis ED, O'Brien SJ, Antunes A. Machado JP, et al. Among authors: antunes a. BMC Genomics. 2016 May 18;17:371. doi: 10.1186/s12864-016-2681-7. BMC Genomics. 2016. PMID: 27193938 Free PMC article.
The era of reference genomes in conservation genomics.
Formenti G, Theissinger K, Fernandes C, Bista I, Bombarely A, Bleidorn C, Ciofi C, Crottini A, Godoy JA, Höglund J, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Mazzoni CJ, Jarvis ED, Bálint M; European Reference Genome Atlas (ERGA) Consortium. Formenti G, et al. Trends Ecol Evol. 2022 Mar;37(3):197-202. doi: 10.1016/j.tree.2021.11.008. Epub 2022 Jan 24. Trends Ecol Evol. 2022. PMID: 35086739 Free article.
Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories.
Bentley BP, Carrasco-Valenzuela T, Ramos EKS, Pawar H, Souza Arantes L, Alexander A, Banerjee SM, Masterson P, Kuhlwilm M, Pippel M, Mountcastle J, Haase B, Uliano-Silva M, Formenti G, Howe K, Chow W, Tracey A, Sims Y, Pelan S, Wood J, Yetsko K, Perrault JR, Stewart K, Benson SR, Levy Y, Todd EV, Shaffer HB, Scott P, Henen BT, Murphy RW, Mohr DW, Scott AF, Duffy DJ, Gemmell NJ, Suh A, Winkler S, Thibaud-Nissen F, Nery MF, Marques-Bonet T, Antunes A, Tikochinski Y, Dutton PH, Fedrigo O, Myers EW, Jarvis ED, Mazzoni CJ, Komoroske LM. Bentley BP, et al. Among authors: antunes a. Proc Natl Acad Sci U S A. 2023 Feb 14;120(7):e2201076120. doi: 10.1073/pnas.2201076120. Epub 2023 Feb 7. Proc Natl Acad Sci U S A. 2023. PMID: 36749728 Free PMC article.
How genomics can help biodiversity conservation.
Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J; European Reference Genome Atlas Consortium. Theissinger K, et al. Trends Genet. 2023 Jul;39(7):545-559. doi: 10.1016/j.tig.2023.01.005. Epub 2023 Feb 16. Trends Genet. 2023. PMID: 36801111 Free article. Review.
1,061 results