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Genome Sequences of Three Phytopathogenic Species of the Magnaporthaceae Family of Fungi.

Okagaki LH, Nunes CC, Sailsbery J, Clay B, Brown D, John T, Oh Y, Young N, Fitzgerald M, Haas BJ, Zeng Q, Young S, Adiconis X, Fan L, Levin JZ, Mitchell TK, Okubara PA, Farman ML, Kohn LM, Birren B, Ma LJ, Dean RA.

G3 (Bethesda). 2015 Sep 28;5(12):2539-45. doi: 10.1534/g3.115.020057.


Massively parallel sequencing of human urinary exosome/microvesicle RNA reveals a predominance of non-coding RNA.

Miranda KC, Bond DT, Levin JZ, Adiconis X, Sivachenko A, Russ C, Brown D, Nusbaum C, Russo LM.

PLoS One. 2014 May 9;9(5):e96094. doi: 10.1371/journal.pone.0096094. eCollection 2014.


Comparative analysis of RNA sequencing methods for degraded or low-input samples.

Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ.

Nat Methods. 2013 Jul;10(7):623-9. doi: 10.1038/nmeth.2483. Epub 2013 May 19. Erratum in: Nat Methods. 2014 Feb;11(2):210.


Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

Shalek AK, Satija R, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A.

Nature. 2013 Jun 13;498(7453):236-40. doi: 10.1038/nature12172. Epub 2013 May 19.


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.

Nat Biotechnol. 2011 May 15;29(7):644-52. doi: 10.1038/nbt.1883.


Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.

Rabani M, Levin JZ, Fan L, Adiconis X, Raychowdhury R, Garber M, Gnirke A, Nusbaum C, Hacohen N, Friedman N, Amit I, Regev A.

Nat Biotechnol. 2011 May;29(5):436-42. doi: 10.1038/nbt.1861. Epub 2011 Apr 24.


Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species.

Yassour M, Pfiffner J, Levin JZ, Adiconis X, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A.

Genome Biol. 2010;11(8):R87. doi: 10.1186/gb-2010-11-8-r87. Epub 2010 Aug 26.


Comprehensive comparative analysis of strand-specific RNA sequencing methods.

Levin JZ, Yassour M, Adiconis X, Nusbaum C, Thompson DA, Friedman N, Gnirke A, Regev A.

Nat Methods. 2010 Sep;7(9):709-15. doi: 10.1038/nmeth.1491. Epub 2010 Aug 15.


Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.

Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A.

Nat Biotechnol. 2010 May;28(5):503-10. doi: 10.1038/nbt.1633. Epub 2010 May 2. Erratum in: Nat Biotechnol. 2010 Jul;28(7):756.


Integrative analysis of the melanoma transcriptome.

Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, Johnson LA, Robinson J, Verhaak RG, Sougnez C, Onofrio RC, Ziaugra L, Cibulskis K, Laine E, Barretina J, Winckler W, Fisher DE, Getz G, Meyerson M, Jaffe DB, Gabriel SB, Lander ES, Dummer R, Gnirke A, Nusbaum C, Garraway LA.

Genome Res. 2010 Apr;20(4):413-27. doi: 10.1101/gr.103697.109. Epub 2010 Feb 23.


Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, Garraway LA, Gnirke A.

Genome Biol. 2009;10(10):R115. doi: 10.1186/gb-2009-10-10-r115. Epub 2009 Oct 16.


Disparities in allele frequencies and population differentiation for 101 disease-associated single nucleotide polymorphisms between Puerto Ricans and non-Hispanic whites.

Mattei J, Parnell LD, Lai CQ, Garcia-Bailo B, Adiconis X, Shen J, Arnett D, Demissie S, Tucker KL, Ordovas JM.

BMC Genet. 2009 Aug 14;10:45. doi: 10.1186/1471-2156-10-45.


Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.

Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A.

Proc Natl Acad Sci U S A. 2009 Mar 3;106(9):3264-9. doi: 10.1073/pnas.0812841106. Epub 2009 Feb 10.


PPARGC1A variation associated with DNA damage, diabetes, and cardiovascular diseases: the Boston Puerto Rican Health Study.

Lai CQ, Tucker KL, Parnell LD, Adiconis X, García-Bailo B, Griffith J, Meydani M, Ordovás JM.

Diabetes. 2008 Apr;57(4):809-16. Epub 2007 Dec 27.


Fenofibrate effect on triglyceride and postprandial response of apolipoprotein A5 variants: the GOLDN study.

Lai CQ, Arnett DK, Corella D, Straka RJ, Tsai MY, Peacock JM, Adiconis X, Parnell LD, Hixson JE, Province MA, Ordovas JM.

Arterioscler Thromb Vasc Biol. 2007 Jun;27(6):1417-25. Epub 2007 Apr 12.


Dietary intake of n-6 fatty acids modulates effect of apolipoprotein A5 gene on plasma fasting triglycerides, remnant lipoprotein concentrations, and lipoprotein particle size: the Framingham Heart Study.

Lai CQ, Corella D, Demissie S, Cupples LA, Adiconis X, Zhu Y, Parnell LD, Tucker KL, Ordovas JM.

Circulation. 2006 May 2;113(17):2062-70. Epub 2006 Apr 24.


Associations between plasma lipid parameters and APOC3 and APOA4 genotypes in a healthy population are independent of dietary cholesterol intake.

Herron KL, Lofgren IE, Adiconis X, Ordovas JM, Fernandez ML.

Atherosclerosis. 2006 Jan;184(1):113-20. Epub 2005 Apr 21.


Genome-wide linkage analyses and candidate gene fine mapping for HDL3 cholesterol: the Framingham Study.

Yang Q, Lai CQ, Parnell L, Cupples LA, Adiconis X, Zhu Y, Wilson PW, Housman DE, Shearman AM, D'Agostino RB, Ordovas JM.

J Lipid Res. 2005 Jul;46(7):1416-25. Epub 2005 Apr 1.


Influence of the APOA5 locus on plasma triglyceride, lipoprotein subclasses, and CVD risk in the Framingham Heart Study.

Lai CQ, Demissie S, Cupples LA, Zhu Y, Adiconis X, Parnell LD, Corella D, Ordovas JM.

J Lipid Res. 2004 Nov;45(11):2096-105. Epub 2004 Sep 1.


Differential effects of the C1431T and Pro12Ala PPARgamma gene variants on plasma lipids and diabetes risk in an Asian population.

Tai ES, Corella D, Deurenberg-Yap M, Adiconis X, Chew SK, Tan CE, Ordovas JM.

J Lipid Res. 2004 Apr;45(4):674-85. Epub 2004 Jan 16.

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