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Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A. Grabherr MG, et al. Among authors: chen z. Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883. Nat Biotechnol. 2011. PMID: 21572440 Free PMC article.
Comparative functional genomics of the fission yeasts.
Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C. Rhind N, et al. Among authors: chen z, chen hm. Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21. Science. 2011. PMID: 21511999 Free PMC article.
Genome analysis of three Pneumocystis species reveals adaptation mechanisms to life exclusively in mammalian hosts.
Ma L, Chen Z, Huang da W, Kutty G, Ishihara M, Wang H, Abouelleil A, Bishop L, Davey E, Deng R, Deng X, Fan L, Fantoni G, Fitzgerald M, Gogineni E, Goldberg JM, Handley G, Hu X, Huber C, Jiao X, Jones K, Levin JZ, Liu Y, Macdonald P, Melnikov A, Raley C, Sassi M, Sherman BT, Song X, Sykes S, Tran B, Walsh L, Xia Y, Yang J, Young S, Zeng Q, Zheng X, Stephens R, Nusbaum C, Birren BW, Azadi P, Lempicki RA, Cuomo CA, Kovacs JA. Ma L, et al. Among authors: chen z. Nat Commun. 2016 Feb 22;7:10740. doi: 10.1038/ncomms10740. Nat Commun. 2016. PMID: 26899007 Free PMC article.
Genome Sequence of Spizellomyces punctatus.
Russ C, Lang BF, Chen Z, Gujja S, Shea T, Zeng Q, Young S, Cuomo CA, Nusbaum C. Russ C, et al. Among authors: chen z. Genome Announc. 2016 Aug 18;4(4):e00849-16. doi: 10.1128/genomeA.00849-16. Genome Announc. 2016. PMID: 27540072 Free PMC article.
Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses.
O'Connell RJ, Thon MR, Hacquard S, Amyotte SG, Kleemann J, Torres MF, Damm U, Buiate EA, Epstein L, Alkan N, Altmüller J, Alvarado-Balderrama L, Bauser CA, Becker C, Birren BW, Chen Z, Choi J, Crouch JA, Duvick JP, Farman MA, Gan P, Heiman D, Henrissat B, Howard RJ, Kabbage M, Koch C, Kracher B, Kubo Y, Law AD, Lebrun MH, Lee YH, Miyara I, Moore N, Neumann U, Nordström K, Panaccione DG, Panstruga R, Place M, Proctor RH, Prusky D, Rech G, Reinhardt R, Rollins JA, Rounsley S, Schardl CL, Schwartz DC, Shenoy N, Shirasu K, Sikhakolli UR, Stüber K, Sukno SA, Sweigard JA, Takano Y, Takahara H, Trail F, van der Does HC, Voll LM, Will I, Young S, Zeng Q, Zhang J, Zhou S, Dickman MB, Schulze-Lefert P, Ver Loren van Themaat E, Ma LJ, Vaillancourt LJ. O'Connell RJ, et al. Among authors: chen z. Nat Genet. 2012 Sep;44(9):1060-5. doi: 10.1038/ng.2372. Epub 2012 Aug 12. Nat Genet. 2012. PMID: 22885923 Free PMC article.
Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection.
Martinez DA, Oliver BG, Gräser Y, Goldberg JM, Li W, Martinez-Rossi NM, Monod M, Shelest E, Barton RC, Birch E, Brakhage AA, Chen Z, Gurr SJ, Heiman D, Heitman J, Kosti I, Rossi A, Saif S, Samalova M, Saunders CW, Shea T, Summerbell RC, Xu J, Young S, Zeng Q, Birren BW, Cuomo CA, White TC. Martinez DA, et al. Among authors: chen z. mBio. 2012 Sep 4;3(5):e00259-12. doi: 10.1128/mBio.00259-12. Print 2012. mBio. 2012. PMID: 22951933 Free PMC article.
The Capsaspora genome reveals a complex unicellular prehistory of animals.
Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I. Suga H, et al. Among authors: chen z. Nat Commun. 2013;4:2325. doi: 10.1038/ncomms3325. Nat Commun. 2013. PMID: 23942320 Free PMC article.
Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus.
Perlin MH, Amselem J, Fontanillas E, Toh SS, Chen Z, Goldberg J, Duplessis S, Henrissat B, Young S, Zeng Q, Aguileta G, Petit E, Badouin H, Andrews J, Razeeq D, Gabaldón T, Quesneville H, Giraud T, Hood ME, Schultz DJ, Cuomo CA. Perlin MH, et al. Among authors: chen z. BMC Genomics. 2015 Jun 16;16(1):461. doi: 10.1186/s12864-015-1660-8. BMC Genomics. 2015. PMID: 26076695 Free PMC article.
The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia.
Muñoz JF, Gauthier GM, Desjardins CA, Gallo JE, Holder J, Sullivan TD, Marty AJ, Carmen JC, Chen Z, Ding L, Gujja S, Magrini V, Misas E, Mitreva M, Priest M, Saif S, Whiston EA, Young S, Zeng Q, Goldman WE, Mardis ER, Taylor JW, McEwen JG, Clay OK, Klein BS, Cuomo CA. Muñoz JF, et al. Among authors: chen z. PLoS Genet. 2015 Oct 6;11(10):e1005493. doi: 10.1371/journal.pgen.1005493. eCollection 2015 Oct. PLoS Genet. 2015. PMID: 26439490 Free PMC article.
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