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Items: 32

1.

Single-cell transcriptomic profiling of the aging mouse brain.

Ximerakis M, Lipnick SL, Innes BT, Simmons SK, Adiconis X, Dionne D, Mayweather BA, Nguyen L, Niziolek Z, Ozek C, Butty VL, Isserlin R, Buchanan SM, Levine SS, Regev A, Bader GD, Levin JZ, Rubin LL.

Nat Neurosci. 2019 Oct;22(10):1696-1708. doi: 10.1038/s41593-019-0491-3. Epub 2019 Sep 24.

PMID:
31551601
2.

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex.

Velasco S, Kedaigle AJ, Simmons SK, Nash A, Rocha M, Quadrato G, Paulsen B, Nguyen L, Adiconis X, Regev A, Levin JZ, Arlotta P.

Nature. 2019 Jun;570(7762):523-527. doi: 10.1038/s41586-019-1289-x. Epub 2019 Jun 5.

PMID:
31168097
3.

Author Correction: Comprehensive comparative analysis of 5'-end RNA-sequencing methods.

Adiconis X, Haber AL, Simmons SK, Moonshine AL, Ji Z, Busby MA, Shi X, Jacques J, Lancaster MA, Pan JQ, Regev A, Levin JZ.

Nat Methods. 2018 Dec;15(12):1126. doi: 10.1038/s41592-018-0237-2.

PMID:
30459407
4.

Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons.

Tekin H, Simmons S, Cummings B, Gao L, Adiconis X, Hession CC, Ghoshal A, Dionne D, Choudhury SR, Yesilyurt V, Sanjana NE, Shi X, Lu C, Heidenreich M, Pan JQ, Levin JZ, Zhang F.

Nat Biomed Eng. 2018 Jul;2(7):540-554. doi: 10.1038/s41551-018-0219-9. Epub 2018 Apr 9.

5.

TBK1 Suppresses RIPK1-Driven Apoptosis and Inflammation during Development and in Aging.

Xu D, Jin T, Zhu H, Chen H, Ofengeim D, Zou C, Mifflin L, Pan L, Amin P, Li W, Shan B, Naito MG, Meng H, Li Y, Pan H, Aron L, Adiconis X, Levin JZ, Yankner BA, Yuan J.

Cell. 2018 Sep 6;174(6):1477-1491.e19. doi: 10.1016/j.cell.2018.07.041. Epub 2018 Aug 23.

6.

Comprehensive comparative analysis of 5'-end RNA-sequencing methods.

Adiconis X, Haber AL, Simmons SK, Levy Moonshine A, Ji Z, Busby MA, Shi X, Jacques J, Lancaster MA, Pan JQ, Regev A, Levin JZ.

Nat Methods. 2018 Jul;15(7):505-511. doi: 10.1038/s41592-018-0014-2. Epub 2018 Jun 4. Erratum in: Nat Methods. 2018 Dec;15(12):1126.

7.

RIPK1 mediates a disease-associated microglial response in Alzheimer's disease.

Ofengeim D, Mazzitelli S, Ito Y, DeWitt JP, Mifflin L, Zou C, Das S, Adiconis X, Chen H, Zhu H, Kelliher MA, Levin JZ, Yuan J.

Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):E8788-E8797. doi: 10.1073/pnas.1714175114. Epub 2017 Sep 13.

8.

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci.

Cuomo CA, Bakkeren G, Khalil HB, Panwar V, Joly D, Linning R, Sakthikumar S, Song X, Adiconis X, Fan L, Goldberg JM, Levin JZ, Young S, Zeng Q, Anikster Y, Bruce M, Wang M, Yin C, McCallum B, Szabo LJ, Hulbert S, Chen X, Fellers JP.

G3 (Bethesda). 2017 Feb 9;7(2):361-376. doi: 10.1534/g3.116.032797.

9.

Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.

Shekhar K, Lapan SW, Whitney IE, Tran NM, Macosko EZ, Kowalczyk M, Adiconis X, Levin JZ, Nemesh J, Goldman M, McCarroll SA, Cepko CL, Regev A, Sanes JR.

Cell. 2016 Aug 25;166(5):1308-1323.e30. doi: 10.1016/j.cell.2016.07.054.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

PMID:
17431185
25.

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.

PMID:
16636175
26.

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.

PMID:
16326171
27.

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.

28.

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.

29.

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.

30.

The APOA5 locus is a strong determinant of plasma triglyceride concentrations across ethnic groups in Singapore.

Lai CQ, Tai ES, Tan CE, Cutter J, Chew SK, Zhu YP, Adiconis X, Ordovas JM.

J Lipid Res. 2003 Dec;44(12):2365-73. Epub 2003 Sep 1.

31.

Polymorphisms at the SRBI locus are associated with lipoprotein levels in subjects with heterozygous familial hypercholesterolemia.

Tai ES, Adiconis X, Ordovas JM, Carmena-Ramon R, Real J, Corella D, Ascaso J, Carmena R.

Clin Genet. 2003 Jan;63(1):53-8.

PMID:
12519372
32.

The TaqIB and -629C>A polymorphisms at the cholesteryl ester transfer protein locus: associations with lipid levels in a multiethnic population. The 1998 Singapore National Health Survey.

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

Clin Genet. 2003 Jan;63(1):19-30.

PMID:
12519368

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