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293 results

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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: marques bonet t. Nat Biotechnol. 2024 Mar;42(3):367-370. doi: 10.1038/s41587-023-02100-3. Nat Biotechnol. 2024. PMID: 38278971 No abstract available.
Towards complete and error-free genome assemblies of all vertebrate species.
Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW 3rd, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnso… See abstract for full author list ➔ Rhie A, et al. Nature. 2021 Apr;592(7856):737-746. doi: 10.1038/s41586-021-03451-0. Epub 2021 Apr 28. Nature. 2021. PMID: 33911273 Free PMC article.
Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.
Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, Brown S, Capodiferro MR, Al-Ajli FO, Ambrosini R, Houde P, Koren S, Oliver K, Smith M, Skelton J, Betteridge E, Dolucan J, Corton C, Bista I, Torrance J, Tracey A, Wood J, Uliano-Silva M, Howe K, McCarthy S, Winkler S, Kwak W, Korlach J, Fungtammasan A, Fordham D, Costa V, Mayes S, Chiara M, Horner DS, Myers E, Durbin R, Achilli A, Braun EL, Phillippy AM, Jarvis ED; Vertebrate Genomes Project Consortium. Formenti G, et al. Genome Biol. 2021 Apr 29;22(1):120. doi: 10.1186/s13059-021-02336-9. Genome Biol. 2021. PMID: 33910595 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.
Reference genomes for conservation.
Paez S, Kraus RHS, Shapiro B, Gilbert MTP, Jarvis ED; Vertebrate Genomes Project Conservation Group; Al-Ajli FO, Ceballos G, Crawford AJ, Fedrigo O, Johnson RN, Johnson WE, Marques-Bonet T, Morin PA, Mueller RC, Ryder OA, Teeling EC, Venkatesh B. Paez S, et al. Science. 2022 Jul 22;377(6604):364-366. doi: 10.1126/science.abm8127. Epub 2022 Jul 21. Science. 2022. PMID: 35862547
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. 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.
Standards recommendations for the Earth BioGenome Project.
Lawniczak MKN, Durbin R, Flicek P, Lindblad-Toh K, Wei X, Archibald JM, Baker WJ, Belov K, Blaxter ML, Marques Bonet T, Childers AK, Coddington JA, Crandall KA, Crawford AJ, Davey RP, Di Palma F, Fang Q, Haerty W, Hall N, Hoff KJ, Howe K, Jarvis ED, Johnson WE, Johnson RN, Kersey PJ, Liu X, Lopez JV, Myers EW, Pettersson OV, Phillippy AM, Poelchau MF, Pruitt KD, Rhie A, Castilla-Rubio JC, Sahu SK, Salmon NA, Soltis PS, Swarbreck D, Thibaud-Nissen F, Wang S, Wegrzyn JL, Zhang G, Zhang H, Lewin HA, Richards S. Lawniczak MKN, et al. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115639118. doi: 10.1073/pnas.2115639118. Proc Natl Acad Sci U S A. 2022. PMID: 35042802 Free PMC article.
The Earth BioGenome Project 2020: Starting the clock.
Lewin HA, Richards S, Lieberman Aiden E, Allende ML, Archibald JM, Bálint M, Barker KB, Baumgartner B, Belov K, Bertorelle G, Blaxter ML, Cai J, Caperello ND, Carlson K, Castilla-Rubio JC, Chaw SM, Chen L, Childers AK, Coddington JA, Conde DA, Corominas M, Crandall KA, Crawford AJ, DiPalma F, Durbin R, Ebenezer TE, Edwards SV, Fedrigo O, Flicek P, Formenti G, Gibbs RA, Gilbert MTP, Goldstein MM, Graves JM, Greely HT, Grigoriev IV, Hackett KJ, Hall N, Haussler D, Helgen KM, Hogg CJ, Isobe S, Jakobsen KS, Janke A, Jarvis ED, Johnson WE, Jones SJM, Karlsson EK, Kersey PJ, Kim JH, Kress WJ, Kuraku S, Lawniczak MKN, Leebens-Mack JH, Li X, Lindblad-Toh K, Liu X, Lopez JV, Marques-Bonet T, Mazard S, Mazet JAK, Mazzoni CJ, Myers EW, O'Neill RJ, Paez S, Park H, Robinson GE, Roquet C, Ryder OA, Sabir JSM, Shaffer HB, Shank TM, Sherkow JS, Soltis PS, Tang B, Tedersoo L, Uliano-Silva M, Wang K, Wei X, Wetzer R, Wilson JL, Xu X, Yang H, Yoder AD, Zhang G. Lewin HA, et al. Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115635118. doi: 10.1073/pnas.2115635118. Proc Natl Acad Sci U S A. 2022. PMID: 35042800 Free PMC article. No abstract available.
293 results