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Page 1
A chromosome-level reference genome and pangenome for barn swallow population genomics.
Secomandi S, Gallo GR, Sozzoni M, Iannucci A, Galati E, Abueg L, Balacco J, Caprioli M, Chow W, Ciofi C, Collins J, Fedrigo O, Ferretti L, Fungtammasan A, Haase B, Howe K, Kwak W, Lombardo G, Masterson P, Messina G, Møller AP, Mountcastle J, Mousseau TA, Ferrer Obiol J, Olivieri A, Rhie A, Rubolini D, Saclier M, Stanyon R, Stucki D, Thibaud-Nissen F, Torrance J, Torroni A, Weber K, Ambrosini R, Bonisoli-Alquati A, Jarvis ED, Gianfranceschi L, Formenti G. Secomandi S, et al. Among authors: jarvis ed. Cell Rep. 2023 Jan 31;42(1):111992. doi: 10.1016/j.celrep.2023.111992. Epub 2023 Jan 19. Cell Rep. 2023. PMID: 36662619 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. Among authors: jarvis ed. 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.
A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.
Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G, Haase B, Mountcastle J, Fedrigo O, Fogg J, Kirilenko B, Munegowda C, Hiller M, Jain A, Kihara D, Rhie A, Phillippy AM, Swanson SA, Jiang P, Clegg DO, Jarvis ED, Thomson JA, Stewart R, Chaisson MJP, Bukhman YV. Toh H, et al. Among authors: jarvis ed. BMC Biol. 2022 Nov 8;20(1):245. doi: 10.1186/s12915-022-01427-8. BMC Biol. 2022. PMID: 36344967 Free PMC article.
The swan genome and transcriptome, it is not all black and white.
Karawita AC, Cheng Y, Chew KY, Challagulla A, Kraus R, Mueller RC, Tong MZW, Hulme KD, Bielefeldt-Ohmann H, Steele LE, Wu M, Sng J, Noye E, Bruxner TJ, Au GG, Lowther S, Blommaert J, Suh A, McCauley AJ, Kaur P, Dudchenko O, Aiden E, Fedrigo O, Formenti G, Mountcastle J, Chow W, Martin FJ, Ogeh DN, Thiaud-Nissen F, Howe K, Tracey A, Smith J, Kuo RI, Renfree MB, Kimura T, Sakoda Y, McDougall M, Spencer HG, Pyne M, Tolf C, Waldenström J, Jarvis ED, Baker ML, Burt DW, Short KR. Karawita AC, et al. Among authors: jarvis ed. Genome Biol. 2023 Jan 23;24(1):13. doi: 10.1186/s13059-022-02838-0. Genome Biol. 2023. PMID: 36683094 Free PMC article.
Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C; Human Pangenome Reference Consortium; Korbel JO, Paten B, Marschall T, Eichler EE. Porubsky D, et al. Genome Res. 2023 Apr;33(4):496-510. doi: 10.1101/gr.277334.122. Epub 2023 May 10. Genome Res. 2023. PMID: 37164484 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: jarvis ed. bioRxiv [Preprint]. 2023 Jun 30:2023.06.28.546576. doi: 10.1101/2023.06.28.546576. bioRxiv. 2023. PMID: 37425881 Free PMC article. Updated. Preprint.
A Chromosome-Level Reference Genome for the Black-Legged Kittiwake (Rissa tridactyla), a Declining Circumpolar Seabird.
Sozzoni M, Ferrer Obiol J, Formenti G, Tigano A, Paris JR, Balacco JR, Jain N, Tilley T, Collins J, Sims Y, Wood J, Benowitz-Fredericks ZM, Field KA, Seyoum E, Gatt MC, Léandri-Breton DJ, Nakajima C, Whelan S, Gianfranceschi L, Hatch SA, Elliott KH, Shoji A, Cecere JG, Jarvis ED, Pilastro A, Rubolini D. Sozzoni M, et al. Among authors: jarvis ed. Genome Biol Evol. 2023 Aug 1;15(8):evad153. doi: 10.1093/gbe/evad153. Genome Biol Evol. 2023. PMID: 37590950 Free PMC article.
Prioritizing Endangered Species in Genome Sequencing: Conservation Genomics in Action with the First Platinum-Standard Reference-Quality Genome of the Critically Endangered European Mink Mustela lutreola L., 1761.
Skorupski J, Brandes F, Seebass C, Festl W, Śmietana P, Balacco J, Jain N, Tilley T, Abueg L, Wood J, Sims Y, Formenti G, Fedrigo O, Jarvis ED. Skorupski J, et al. Among authors: jarvis ed. Int J Mol Sci. 2023 Oct 1;24(19):14816. doi: 10.3390/ijms241914816. Int J Mol Sci. 2023. PMID: 37834264 Free PMC article.
232 results