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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.
Nat Biotechnol. 2024 Mar;42(3):367-370. doi: 10.1038/s41587-023-02100-3.
Nat Biotechnol. 2024.
PMID: 38278971
No abstract available.
A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.
Rice ES, Alberdi A, Alfieri J, Athrey G, Balacco JR, Bardou P, Blackmon H, Charles M, Cheng HH, Fedrigo O, Fiddaman SR, Formenti G, Frantz LAF, Gilbert MTP, Hearn CJ, Jarvis ED, Klopp C, Marcos S, Mason AS, Velez-Irizarry D, Xu L, Warren WC.
Rice ES, et al. Among authors: balacco jr.
BMC Biol. 2023 Nov 22;21(1):267. doi: 10.1186/s12915-023-01758-0.
BMC Biol. 2023.
PMID: 37993882
Free PMC article.
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Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.
Sendell-Price AT, Tulenko FJ, Pettersson M, Kang D, Montandon M, Winkler S, Kulb K, Naylor GP, Phillippy A, Fedrigo O, Mountcastle J, Balacco JR, Dutra A, Dale RE, Haase B, Jarvis ED, Myers G, Burgess SM, Currie PD, Andersson L, Schartl M.
Sendell-Price AT, et al. Among authors: balacco jr.
Nat Commun. 2023 Oct 19;14(1):6628. doi: 10.1038/s41467-023-42238-x.
Nat Commun. 2023.
PMID: 37857613
Free PMC article.
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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: balacco jr.
Genome Biol Evol. 2023 Aug 1;15(8):evad153. doi: 10.1093/gbe/evad153.
Genome Biol Evol. 2023.
PMID: 37590950
Free PMC article.
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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, 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: balacco jr.
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.
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An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.
Timoshevskaya N, Eşkut KI, Timoshevskiy VA, Robb SMC, Holt C, Hess JE, Parker HJ, Baker CF, Miller AK, Saraceno C, Yandell M, Krumlauf R, Narum SR, Lampman RT, Gemmell NJ, Mountcastle J, Haase B, Balacco JR, Formenti G, Pelan S, Sims Y, Howe K, Fedrigo O, Jarvis ED, Smith JJ.
Timoshevskaya N, et al. Among authors: balacco jr.
Cell Rep. 2023 Mar 28;42(3):112263. doi: 10.1016/j.celrep.2023.112263. Epub 2023 Mar 15.
Cell Rep. 2023.
PMID: 36930644
Free PMC article.
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Mycorrhizal Infection Can Ameliorate Abiotic Factors in Urban Soils.
Balacco JR, Vaidya BP, Hagmann DF, Goodey NM, Krumins JA.
Balacco JR, et al.
Microb Ecol. 2023 Jan;85(1):100-107. doi: 10.1007/s00248-021-01945-y. Epub 2022 Jan 8.
Microb Ecol. 2023.
PMID: 34997311
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Reference genome and demographic history of the most endangered marine mammal, the vaquita.
Morin PA, Archer FI, Avila CD, Balacco JR, Bukhman YV, Chow W, Fedrigo O, Formenti G, Fronczek JA, Fungtammasan A, Gulland FMD, Haase B, Peter Heide-Jorgensen M, Houck ML, Howe K, Misuraca AC, Mountcastle J, Musser W, Paez S, Pelan S, Phillippy A, Rhie A, Robinson J, Rojas-Bracho L, Rowles TK, Ryder OA, Smith CR, Stevenson S, Taylor BL, Teilmann J, Torrance J, Wells RS, Westgate AJ, Jarvis ED.
Morin PA, et al. Among authors: balacco jr.
Mol Ecol Resour. 2021 May;21(4):1008-1020. doi: 10.1111/1755-0998.13284. Epub 2020 Nov 20.
Mol Ecol Resour. 2021.
PMID: 33089966
Free PMC article.
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