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Items: 1 to 50 of 102

1.

Robust single-cell DNA methylome profiling with snmC-seq2.

Luo C, Rivkin A, Zhou J, Sandoval JP, Kurihara L, Lucero J, Castanon R, Nery JR, Pinto-Duarte A, Bui B, Fitzpatrick C, O'Connor C, Ruga S, Van Eden ME, Davis DA, Mash DC, Behrens MM, Ecker JR.

Nat Commun. 2018 Sep 20;9(1):3824. doi: 10.1038/s41467-018-06355-2.

PMID:
30237449
2.

Transcriptional and epigenomic landscapes of CNS and non-CNS vascular endothelial cells.

Sabbagh MF, Heng JS, Luo C, Castanon RG, Nery JR, Rattner A, Goff LA, Ecker JR, Nathans J.

Elife. 2018 Sep 6;7. pii: e36187. doi: 10.7554/eLife.36187.

3.

Dynamic DNA methylation reconfiguration during seed development and germination.

Kawakatsu T, Nery JR, Castanon R, Ecker JR.

Genome Biol. 2017 Sep 15;18(1):171. doi: 10.1186/s13059-017-1251-x.

4.

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex.

Luo C, Keown CL, Kurihara L, Zhou J, He Y, Li J, Castanon R, Lucero J, Nery JR, Sandoval JP, Bui B, Sejnowski TJ, Harkins TT, Mukamel EA, Behrens MM, Ecker JR.

Science. 2017 Aug 11;357(6351):600-604. doi: 10.1126/science.aan3351.

5.

Mapping genome-wide transcription-factor binding sites using DAP-seq.

Bartlett A, O'Malley RC, Huang SC, Galli M, Nery JR, Gallavotti A, Ecker JR.

Nat Protoc. 2017 Aug;12(8):1659-1672. doi: 10.1038/nprot.2017.055. Epub 2017 Jul 20.

6.

CrY2H-seq: a massively multiplexed assay for deep-coverage interactome mapping.

Trigg SA, Garza RM, MacWilliams A, Nery JR, Bartlett A, Castanon R, Goubil A, Feeney J, O'Malley R, Huang SC, Zhang ZZ, Galli M, Ecker JR.

Nat Methods. 2017 Aug;14(8):819-825. doi: 10.1038/nmeth.4343. Epub 2017 Jun 26.

7.

Allele-specific non-CG DNA methylation marks domains of active chromatin in female mouse brain.

Keown CL, Berletch JB, Castanon R, Nery JR, Disteche CM, Ecker JR, Mukamel EA.

Proc Natl Acad Sci U S A. 2017 Apr 4;114(14):E2882-E2890. doi: 10.1073/pnas.1611905114. Epub 2017 Mar 20.

8.

Improved regulatory element prediction based on tissue-specific local epigenomic signatures.

He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR.

Proc Natl Acad Sci U S A. 2017 Feb 28;114(9):E1633-E1640. doi: 10.1073/pnas.1618353114. Epub 2017 Feb 13.

9.

Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain.

Luo C, Lancaster MA, Castanon R, Nery JR, Knoblich JA, Ecker JR.

Cell Rep. 2016 Dec 20;17(12):3369-3384. doi: 10.1016/j.celrep.2016.12.001.

10.

A transcription factor hierarchy defines an environmental stress response network.

Song L, Huang SC, Wise A, Castanon R, Nery JR, Chen H, Watanabe M, Thomas J, Bar-Joseph Z, Ecker JR.

Science. 2016 Nov 4;354(6312). pii: aag1550.

11.

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR.

Cell. 2016 Sep 8;166(6):1598. doi: 10.1016/j.cell.2016.08.063. Epub 2016 Sep 8. No abstract available.

12.

Integration of omic networks in a developmental atlas of maize.

Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP.

Science. 2016 Aug 19;353(6301):814-8. doi: 10.1126/science.aag1125.

13.

Molecular Criteria for Defining the Naive Human Pluripotent State.

Theunissen TW, Friedli M, He Y, Planet E, O'Neil RC, Markoulaki S, Pontis J, Wang H, Iouranova A, Imbeault M, Duc J, Cohen MA, Wert KJ, Castanon R, Zhang Z, Huang Y, Nery JR, Drotar J, Lungjangwa T, Trono D, Ecker JR, Jaenisch R.

Cell Stem Cell. 2016 Oct 6;19(4):502-515. doi: 10.1016/j.stem.2016.06.011. Epub 2016 Jul 14.

14.

Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions.

Kawakatsu T, Huang SC, Jupe F, Sasaki E, Schmitz RJ, Urich MA, Castanon R, Nery JR, Barragan C, He Y, Chen H, Dubin M, Lee CR, Wang C, Bemm F, Becker C, O'Neil R, O'Malley RC, Quarless DX; 1001 Genomes Consortium, Schork NJ, Weigel D, Nordborg M, Ecker JR.

Cell. 2016 Jul 14;166(2):492-505. doi: 10.1016/j.cell.2016.06.044.

15.

Unique cell-type-specific patterns of DNA methylation in the root meristem.

Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, Ecker JR.

Nat Plants. 2016 Apr 29;2(5):16058. doi: 10.1038/nplants.2016.58.

16.

Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape.

O'Malley RC, Huang SC, Song L, Lewsey MG, Bartlett A, Nery JR, Galli M, Gallavotti A, Ecker JR.

Cell. 2016 May 19;165(5):1280-1292. doi: 10.1016/j.cell.2016.04.038. Erratum in: Cell. 2016 Sep 8;166(6):1598.

17.

Epigenomic landscapes of retinal rods and cones.

Mo A, Luo C, Davis FP, Mukamel EA, Henry GL, Nery JR, Urich MA, Picard S, Lister R, Eddy SR, Beer MA, Ecker JR, Nathans J.

Elife. 2016 Mar 7;5:e11613. doi: 10.7554/eLife.11613.

18.

Mobile small RNAs regulate genome-wide DNA methylation.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR.

Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):E801-10. doi: 10.1073/pnas.1515072113. Epub 2016 Jan 19.

19.

Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light.

Pedmale UV, Huang SC, Zander M, Cole BJ, Hetzel J, Ljung K, Reis PAB, Sridevi P, Nito K, Nery JR, Ecker JR, Chory J.

Cell. 2016 Jan 14;164(1-2):233-245. doi: 10.1016/j.cell.2015.12.018. Epub 2015 Dec 24.

20.

Corrigendum: Human body epigenome maps reveal noncanonical DNA methylation variation.

Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, Ren B, Sejnowski TJ, Wang W, Ecker JR.

Nature. 2016 Feb 11;530(7589):242. doi: 10.1038/nature16179. Epub 2015 Nov 25. No abstract available.

PMID:
26605523
21.

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain.

Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, Eddy SR, Ecker JR, Nathans J.

Neuron. 2015 Jun 17;86(6):1369-84. doi: 10.1016/j.neuron.2015.05.018.

22.

Human body epigenome maps reveal noncanonical DNA methylation variation.

Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, Lin S, Lin Y, Jung I, Schmitt AD, Selvaraj S, Ren B, Sejnowski TJ, Wang W, Ecker JR.

Nature. 2015 Jul 9;523(7559):212-6. doi: 10.1038/nature14465. Epub 2015 Jun 1. Erratum in: Nature. 2016 Feb 11;530(7589):242.

23.

An alternative pluripotent state confers interspecies chimaeric competency.

Wu J, Okamura D, Li M, Suzuki K, Luo C, Ma L, He Y, Li Z, Benner C, Tamura I, Krause MN, Nery JR, Du T, Zhang Z, Hishida T, Takahashi Y, Aizawa E, Kim NY, Lajara J, Guillen P, Campistol JM, Esteban CR, Ross PJ, Saghatelian A, Ren B, Ecker JR, Izpisua Belmonte JC.

Nature. 2015 May 21;521(7552):316-21. doi: 10.1038/nature14413. Epub 2015 May 6.

24.

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing.

Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR.

Nat Protoc. 2015 Mar;10(3):475-83. doi: 10.1038/nprot.2014.114. Epub 2015 Feb 18.

25.

Comparison of the transcriptional landscapes between human and mouse tissues.

Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP.

Proc Natl Acad Sci U S A. 2014 Dec 2;111(48):17224-9. doi: 10.1073/pnas.1413624111. Epub 2014 Nov 20.

26.

The developmental potential of iPSCs is greatly influenced by reprogramming factor selection.

Buganim Y, Markoulaki S, van Wietmarschen N, Hoke H, Wu T, Ganz K, Akhtar-Zaidi B, He Y, Abraham BJ, Porubsky D, Kulenkampff E, Faddah DA, Shi L, Gao Q, Sarkar S, Cohen M, Goldmann J, Nery JR, Schultz MD, Ecker JR, Xiao A, Young RA, Lansdorp PM, Jaenisch R.

Cell Stem Cell. 2014 Sep 4;15(3):295-309. doi: 10.1016/j.stem.2014.07.003.

27.

Abnormalities in human pluripotent cells due to reprogramming mechanisms.

Ma H, Morey R, O'Neil RC, He Y, Daughtry B, Schultz MD, Hariharan M, Nery JR, Castanon R, Sabatini K, Thiagarajan RD, Tachibana M, Kang E, Tippner-Hedges R, Ahmed R, Gutierrez NM, Van Dyken C, Polat A, Sugawara A, Sparman M, Gokhale S, Amato P, Wolf DP, Ecker JR, Laurent LC, Mitalipov S.

Nature. 2014 Jul 10;511(7508):177-83. doi: 10.1038/nature13551. Epub 2014 Jul 2.

28.

Global epigenomic reconfiguration during mammalian brain development.

Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, Yu M, Tonti-Filippini J, Heyn H, Hu S, Wu JC, Rao A, Esteller M, He C, Haghighi FG, Sejnowski TJ, Behrens MM, Ecker JR.

Science. 2013 Aug 9;341(6146):1237905. doi: 10.1126/science.1237905. Epub 2013 Jul 4.

29.

Temporal transcriptional response to ethylene gas drives growth hormone cross-regulation in Arabidopsis.

Chang KN, Zhong S, Weirauch MT, Hon G, Pelizzola M, Li H, Huang SS, Schmitz RJ, Urich MA, Kuo D, Nery JR, Qiao H, Yang A, Jamali A, Chen H, Ideker T, Ren B, Bar-Joseph Z, Hughes TR, Ecker JR.

Elife. 2013 Jun 11;2:e00675. doi: 10.7554/eLife.00675.

30.

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population.

Schmitz RJ, He Y, Valdés-López O, Khan SM, Joshi T, Urich MA, Nery JR, Diers B, Xu D, Stacey G, Ecker JR.

Genome Res. 2013 Oct;23(10):1663-74. doi: 10.1101/gr.152538.112. Epub 2013 Jun 5.

31.

Epigenomic analysis of multilineage differentiation of human embryonic stem cells.

Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B.

Cell. 2013 May 23;153(5):1134-48. doi: 10.1016/j.cell.2013.04.022. Epub 2013 May 9.

32.

Patterns of population epigenomic diversity.

Schmitz RJ, Schultz MD, Urich MA, Nery JR, Pelizzola M, Libiger O, Alix A, McCosh RB, Chen H, Schork NJ, Ecker JR.

Nature. 2013 Mar 14;495(7440):193-8. doi: 10.1038/nature11968. Epub 2013 Mar 6.

33.

Widespread dynamic DNA methylation in response to biotic stress.

Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR.

Proc Natl Acad Sci U S A. 2012 Aug 7;109(32):E2183-91. doi: 10.1073/pnas.1209329109. Epub 2012 Jun 25.

34.

Surveillance of 3' Noncoding Transcripts Requires FIERY1 and XRN3 in Arabidopsis.

Kurihara Y, Schmitz RJ, Nery JR, Schultz MD, Okubo-Kurihara E, Morosawa T, Tanaka M, Toyoda T, Seki M, Ecker JR.

G3 (Bethesda). 2012 Apr;2(4):487-98. doi: 10.1534/g3.111.001362. Epub 2012 Apr 1.

35.

(210)Pb and composition data of near-surface sediments and interstitial waters evidencing anthropogenic inputs in Amazon River mouth, Macapá, Brazil.

Nery JR, Bonotto DM.

J Environ Radioact. 2011 Apr;102(4):348-62. doi: 10.1016/j.jenvrad.2011.01.008. Epub 2011 Feb 25.

PMID:
21353731
36.

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells.

Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O'Malley R, Castanon R, Klugman S, Downes M, Yu R, Stewart R, Ren B, Thomson JA, Evans RM, Ecker JR.

Nature. 2011 Mar 3;471(7336):68-73. doi: 10.1038/nature09798. Epub 2011 Feb 2. Erratum in: Nature. 2014 Oct 2;514(7520):126.

37.

Human DNA methylomes at base resolution show widespread epigenomic differences.

Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR.

Nature. 2009 Nov 19;462(7271):315-22. doi: 10.1038/nature08514. Epub 2009 Oct 14.

38.

Piggyback technique in adult orthotopic liver transplantation: an analysis of 1067 liver transplants at a single center.

Nishida S, Nakamura N, Vaidya A, Levi DM, Kato T, Nery JR, Madariaga JR, Molina E, Ruiz P, Gyamfi A, Tzakis AG.

HPB (Oxford). 2006;8(3):182-8. doi: 10.1080/13651820500542135.

39.

Bacterial infections after intestine and multivisceral transplantation. The experience of the University of Miami (1994-2001).

Loinaz C, Kato T, Nishida S, Weppler D, Levi D, Dowdy L, Nery JR, Mittal N, Vianna R, Fortún J, De la Cruz J, Madariaga J, Tzakis A.

Hepatogastroenterology. 2006 Mar-Apr;53(68):234-42.

PMID:
16608031
40.

Prolonged clamping of the liver parenchyma: a salvage maneuver in exsanguinating liver injury.

Ginzburg E, Klein Y, Sutherland M, Levi D, Nery JR, Sleeman D, Shatz DV, Lynn M, Goldberg D, Cohn SM.

J Trauma. 2004 Apr;56(4):922-3. No abstract available.

PMID:
15187765
41.

Intestinal and multivisceral transplantation after abdominal trauma.

Nishida S, Hadjis NS, Levi DM, Kato T, Vaidya A, Nery JR, Madariaga J, Nakamura N, Ruiz P, Neff G, Byers P, Tzakis AG.

J Trauma. 2004 Feb;56(2):323-7.

PMID:
14960974
42.

Donor intracaval thrombus formation and pulmonary embolism after simultaneous piggyback liver transplantation and aortic valve replacement.

Nishida S, Vaidya A, Franco E, Neff G, Madariaga J, Nakamura N, Levi DM, Nery JR, Bolooki H, Tzakis AG.

Clin Transplant. 2003 Oct;17(5):465-8.

PMID:
14703932
43.

Bacterial infections after intestine and multivisceral transplantation.

Loinaz C, Kato T, Nishida S, Weppler D, Levi D, Dowdy L, Madariaga J, Nery JR, Vianna R, Mittal N, Tzakis A.

Transplant Proc. 2003 Aug;35(5):1929-30.

PMID:
12962852
44.

Intestinal transplantation: advances in immunosuppression and surgical techniques.

Tzakis AG, Tryphonopoulos P, Kato T, Nishida S, Levi DM, Nery JR, Madariaga J, De Faria W, Mittal N, Thompson JF, Ruiz P.

Transplant Proc. 2003 Aug;35(5):1925-6.

PMID:
12962850
45.

Alemtuzumab (Campath-1H) combined with tacrolimus in intestinal and multivisceral transplantation.

Tzakis AG, Kato T, Nishida S, Levi DM, Tryphonopoulos P, Madariaga JR, De Faria W, Nery JR, Regev A, Vianna R, Miller J, Esquenazi V, Weppler D, Ruiz P.

Transplantation. 2003 May 15;75(9):1512-7.

PMID:
12792506
46.

Preliminary experience with campath 1H (C1H) in intestinal and liver transplantation.

Tzakis AG, Kato T, Nishida S, Levi DM, Madariaga JR, Nery JR, Mittal N, Regev A, Cantwell P, Gyamfi A, Weppler D, Miller J, Tryphonopoulos P, Ruiz P.

Transplantation. 2003 Apr 27;75(8):1227-31.

PMID:
12717207
47.

Use of liver grafts from donors positive for antihepatitis B-core antibody (anti-HBc) in the era of prophylaxis with hepatitis-B immunoglobulin and lamivudine.

Nery JR, Nery-Avila C, Reddy KR, Cirocco R, Weppler D, Levi DM, Nishida S, Madariaga J, Kato T, Ruiz P, Schiff E, Tzakis AG.

Transplantation. 2003 Apr 27;75(8):1179-86.

PMID:
12717200
48.

Portal versus systemic drainage of small bowel allografts: comparative assessment of survival, function, rejection, and bacterial translocation.

Berney T, Kato T, Nishida S, Tector AJ, Mittal NK, Madariaga J, Nery JR, Cantwell GP, Ruiz P, Tzakis AG.

J Am Coll Surg. 2002 Dec;195(6):804-13.

PMID:
12495313
49.

Successful treatment of posttransplant lymphoproliferative disease with prolonged rituximab treatment in intestinal transplant recipients.

Berney T, Delis S, Kato T, Nishida S, Mittal NK, Madariaga J, Levi D, Nery JR, Cirocco RE, Gelman B, Ruiz P, Tzakis AG.

Transplantation. 2002 Oct 15;74(7):1000-6.

PMID:
12394845
50.

Internal hernia of the small bowel around infrarenal arterial conduits after liver transplantation.

Nishida S, Pinna AG, Nery JR, Levi D, Kato T, Madariaga J, Tzakis AG.

Clin Transplant. 2002 Oct;16(5):334-8.

PMID:
12225429

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