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Evolutionary constraint and innovation across hundreds of placental mammals.
Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR; Zoonomia Consortium§; Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Christmas MJ, et al. Among authors: johnson j. Science. 2023 Apr 28;380(6643):eabn3943. doi: 10.1126/science.abn3943. Epub 2023 Apr 28. Science. 2023. PMID: 37104599 Free PMC article.
The genome of the green anole lizard and a comparative analysis with birds and mammals.
Alföldi J, Di Palma F, Grabherr M, Williams C, Kong L, Mauceli E, Russell P, Lowe CB, Glor RE, Jaffe JD, Ray DA, Boissinot S, Shedlock AM, Botka C, Castoe TA, Colbourne JK, Fujita MK, Moreno RG, ten Hallers BF, Haussler D, Heger A, Heiman D, Janes DE, Johnson J, de Jong PJ, Koriabine MY, Lara M, Novick PA, Organ CL, Peach SE, Poe S, Pollock DD, de Queiroz K, Sanger T, Searle S, Smith JD, Smith Z, Swofford R, Turner-Maier J, Wade J, Young S, Zadissa A, Edwards SV, Glenn TC, Schneider CJ, Losos JB, Lander ES, Breen M, Ponting CP, Lindblad-Toh K. Alföldi J, et al. Among authors: johnson j. Nature. 2011 Aug 31;477(7366):587-91. doi: 10.1038/nature10390. Nature. 2011. PMID: 21881562 Free PMC article.
The genomic basis of adaptive evolution in threespine sticklebacks.
Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, Johnson J, Swofford R, Pirun M, Zody MC, White S, Birney E, Searle S, Schmutz J, Grimwood J, Dickson MC, Myers RM, Miller CT, Summers BR, Knecht AK, Brady SD, Zhang H, Pollen AA, Howes T, Amemiya C; Broad Institute Genome Sequencing Platform & Whole Genome Assembly Team; Baldwin J, Bloom T, Jaffe DB, Nicol R, Wilkinson J, Lander ES, Di Palma F, Lindblad-Toh K, Kingsley DM. Jones FC, et al. Among authors: johnson j. Nature. 2012 Apr 4;484(7392):55-61. doi: 10.1038/nature10944. Nature. 2012. PMID: 22481358 Free PMC article.
The African coelacanth genome provides insights into tetrapod evolution.
Amemiya CT, Alföldi J, Lee AP, Fan S, Philippe H, Maccallum I, Braasch I, Manousaki T, Schneider I, Rohner N, Organ C, Chalopin D, Smith JJ, Robinson M, Dorrington RA, Gerdol M, Aken B, Biscotti MA, Barucca M, Baurain D, Berlin AM, Blatch GL, Buonocore F, Burmester T, Campbell MS, Canapa A, Cannon JP, Christoffels A, De Moro G, Edkins AL, Fan L, Fausto AM, Feiner N, Forconi M, Gamieldien J, Gnerre S, Gnirke A, Goldstone JV, Haerty W, Hahn ME, Hesse U, Hoffmann S, Johnson J, Karchner SI, Kuraku S, Lara M, Levin JZ, Litman GW, Mauceli E, Miyake T, Mueller MG, Nelson DR, Nitsche A, Olmo E, Ota T, Pallavicini A, Panji S, Picone B, Ponting CP, Prohaska SJ, Przybylski D, Saha NR, Ravi V, Ribeiro FJ, Sauka-Spengler T, Scapigliati G, Searle SM, Sharpe T, Simakov O, Stadler PF, Stegeman JJ, Sumiyama K, Tabbaa D, Tafer H, Turner-Maier J, van Heusden P, White S, Williams L, Yandell M, Brinkmann H, Volff JN, Tabin CJ, Shubin N, Schartl M, Jaffe DB, Postlethwait JH, Venkatesh B, Di Palma F, Lander ES, Meyer A, Lindblad-Toh K. Amemiya CT, et al. Among authors: johnson j. Nature. 2013 Apr 18;496(7445):311-6. doi: 10.1038/nature12027. Nature. 2013. PMID: 23598338 Free PMC article.
An improved canine genome and a comprehensive catalogue of coding genes and non-coding transcripts.
Hoeppner MP, Lundquist A, Pirun M, Meadows JR, Zamani N, Johnson J, Sundström G, Cook A, FitzGerald MG, Swofford R, Mauceli E, Moghadam BT, Greka A, Alföldi J, Abouelleil A, Aftuck L, Bessette D, Berlin A, Brown A, Gearin G, Lui A, Macdonald JP, Priest M, Shea T, Turner-Maier J, Zimmer A, Lander ES, di Palma F, Lindblad-Toh K, Grabherr MG. Hoeppner MP, et al. Among authors: johnson j. PLoS One. 2014 Mar 13;9(3):e91172. doi: 10.1371/journal.pone.0091172. eCollection 2014. PLoS One. 2014. PMID: 24625832 Free PMC article.
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.
Carneiro M, Rubin CJ, Di Palma F, Albert FW, Alföldi J, Martinez Barrio A, Pielberg G, Rafati N, Sayyab S, Turner-Maier J, Younis S, Afonso S, Aken B, Alves JM, Barrell D, Bolet G, Boucher S, Burbano HA, Campos R, Chang JL, Duranthon V, Fontanesi L, Garreau H, Heiman D, Johnson J, Mage RG, Peng Z, Queney G, Rogel-Gaillard C, Ruffier M, Searle S, Villafuerte R, Xiong A, Young S, Forsberg-Nilsson K, Good JM, Lander ES, Ferrand N, Lindblad-Toh K, Andersson L. Carneiro M, et al. Among authors: johnson j. Science. 2014 Aug 29;345(6200):1074-1079. doi: 10.1126/science.1253714. Science. 2014. PMID: 25170157 Free PMC article.
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease.
Peng X, Alföldi J, Gori K, Eisfeld AJ, Tyler SR, Tisoncik-Go J, Brawand D, Law GL, Skunca N, Hatta M, Gasper DJ, Kelly SM, Chang J, Thomas MJ, Johnson J, Berlin AM, Lara M, Russell P, Swofford R, Turner-Maier J, Young S, Hourlier T, Aken B, Searle S, Sun X, Yi Y, Suresh M, Tumpey TM, Siepel A, Wisely SM, Dessimoz C, Kawaoka Y, Birren BW, Lindblad-Toh K, Di Palma F, Engelhardt JF, Palermo RE, Katze MG. Peng X, et al. Among authors: johnson j. Nat Biotechnol. 2014 Dec;32(12):1250-5. doi: 10.1038/nbt.3079. Epub 2014 Nov 17. Nat Biotechnol. 2014. PMID: 25402615 Free PMC article.
Exome sequencing of lymphomas from three dog breeds reveals somatic mutation patterns reflecting genetic background.
Elvers I, Turner-Maier J, Swofford R, Koltookian M, Johnson J, Stewart C, Zhang CZ, Schumacher SE, Beroukhim R, Rosenberg M, Thomas R, Mauceli E, Getz G, Palma FD, Modiano JF, Breen M, Lindblad-Toh K, Alföldi J. Elvers I, et al. Among authors: johnson j. Genome Res. 2015 Nov;25(11):1634-45. doi: 10.1101/gr.194449.115. Epub 2015 Sep 16. Genome Res. 2015. PMID: 26377837 Free PMC article.
An Improved microRNA Annotation of the Canine Genome.
Penso-Dolfin L, Swofford R, Johnson J, Alföldi J, Lindblad-Toh K, Swarbreck D, Moxon S, Di Palma F. Penso-Dolfin L, et al. Among authors: johnson j. PLoS One. 2016 Apr 27;11(4):e0153453. doi: 10.1371/journal.pone.0153453. eCollection 2016. PLoS One. 2016. PMID: 27119849 Free PMC article.
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