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Items: 1 to 20 of 106

1.

Cross-Platform DNA Encoding for Single-Cell Imaging of Gene Expression.

Zrazhevskiy P, Akilesh S, Tai W, Queitsch K, True LD, Fromm J, Wu D, Nelson P, Stamatoyannopoulos JA, Gao X.

Angew Chem Int Ed Engl. 2016 Jun 7. doi: 10.1002/anie.201603945. [Epub ahead of print]

PMID:
27273345
2.

Taking Stock of Regulatory Variation.

Maurano MT, Stamatoyannopoulos JA.

Cell Syst. 2015 Jul 29;1(1):18-21. doi: 10.1016/j.cels.2015.07.011. Epub 2015 Jul 29.

PMID:
27135686
3.

Operating on Genomic Ranges Using BEDOPS.

Neph S, Reynolds AP, Kuehn MS, Stamatoyannopoulos JA.

Methods Mol Biol. 2016;1418:267-81. doi: 10.1007/978-1-4939-3578-9_14.

PMID:
27008020
4.

Genomic footprinting.

Vierstra J, Stamatoyannopoulos JA.

Nat Methods. 2016 Mar;13(3):213-21. doi: 10.1038/nmeth.3768.

PMID:
26914205
5.

Genetic association of long-chain acyl-CoA synthetase 1 variants with fasting glucose, diabetes, and subclinical atherosclerosis.

Manichaikul A, Wang XQ, Zhao W, Wojczynski MK, Siebenthall K, Stamatoyannopoulos JA, Saleheen D, Borecki IB, Reilly MP, Rich SS, Bornfeldt KE.

J Lipid Res. 2016 Mar;57(3):433-42. doi: 10.1194/jlr.M064592. Epub 2015 Dec 28.

PMID:
26711138
6.

Erratum: Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.

Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA.

Nat Genet. 2016 Jan;48(1):101. doi: 10.1038/ng0116-101c. No abstract available.

PMID:
26711113
7.

Local compartment changes and regulatory landscape alterations in histone H1-depleted cells.

Geeven G, Zhu Y, Kim BJ, Bartholdy BA, Yang SM, Macfarlan TS, Gifford WD, Pfaff SL, Verstegen MJ, Pinto H, Vermunt MW, Creyghton MP, Wijchers PJ, Stamatoyannopoulos JA, Skoultchi AI, de Laat W.

Genome Biol. 2015 Dec 23;16:289. doi: 10.1186/s13059-015-0857-0.

8.

Corrigendum: Domains of genome-wide gene expression dysregulation in Down's syndrome.

Letourneau A, Santoni FA, Bonilla X, Sailani MR, Gonzalez D, Kind J, Chevalier C, Thurman R, Sandstrom RS, Hibaoui Y, Garieri M, Popadin K, Falconnet E, Gagnebin M, Gehrig C, Vannier A, Guipponi M, Farinelli L, Robyr D, Migliavacca E, Borel C, Deutsch S, Feki A, Stamatoyannopoulos JA, Herault Y, van Steensel B, Guigo R, Antonarakis SE.

Nature. 2016 Mar 17;531(7594):400. doi: 10.1038/nature16135. Epub 2015 Dec 2. No abstract available.

PMID:
26633627
9.

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.

Maurano MT, Haugen E, Sandstrom R, Vierstra J, Shafer A, Kaul R, Stamatoyannopoulos JA.

Nat Genet. 2015 Dec;47(12):1393-401. doi: 10.1038/ng.3432. Epub 2015 Oct 26. Erratum in: Nat Genet. 2016 Jan;48(1):101.

10.

Functional footprinting of regulatory DNA.

Vierstra J, Reik A, Chang KH, Stehling-Sun S, Zhou Y, Hinkley SJ, Paschon DE, Zhang L, Psatha N, Bendana YR, O'Neil CM, Song AH, Mich AK, Liu PQ, Lee G, Bauer DE, Holmes MC, Orkin SH, Papayannopoulou T, Stamatoyannopoulos G, Rebar EJ, Gregory PD, Urnov FD, Stamatoyannopoulos JA.

Nat Methods. 2015 Oct;12(10):927-30. doi: 10.1038/nmeth.3554. Epub 2015 Aug 31.

PMID:
26322838
11.

Role of DNA Methylation in Modulating Transcription Factor Occupancy.

Maurano MT, Wang H, John S, Shafer A, Canfield T, Lee K, Stamatoyannopoulos JA.

Cell Rep. 2015 Aug 18;12(7):1184-95. doi: 10.1016/j.celrep.2015.07.024. Epub 2015 Aug 6.

12.

2p15-p16.1 microdeletions encompassing and proximal to BCL11A are associated with elevated HbF in addition to neurologic impairment.

Funnell AP, Prontera P, Ottaviani V, Piccione M, Giambona A, Maggio A, Ciaffoni F, Stehling-Sun S, Marra M, Masiello F, Varricchio L, Stamatoyannopoulos JA, Migliaccio AR, Papayannopoulou T.

Blood. 2015 Jul 2;126(1):89-93. doi: 10.1182/blood-2015-04-638528. Epub 2015 May 27.

PMID:
26019277
13.

Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution.

Mayer A, di Iulio J, Maleri S, Eser U, Vierstra J, Reynolds A, Sandstrom R, Stamatoyannopoulos JA, Churchman LS.

Cell. 2015 Apr 23;161(3):541-54. doi: 10.1016/j.cell.2015.03.010.

14.

Cell-of-origin chromatin organization shapes the mutational landscape of cancer.

Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence MS, Reynolds A, Rynes E, Vlahoviček K, Stamatoyannopoulos JA, Sunyaev SR.

Nature. 2015 Feb 19;518(7539):360-4. doi: 10.1038/nature14221.

15.

Integrative analysis of 111 reference human epigenomes.

Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M.

Nature. 2015 Feb 19;518(7539):317-30. doi: 10.1038/nature14248.

16.

Dynamics of chromatin accessibility and long-range interactions in response to glucocorticoid pulsing.

Stavreva DA, Coulon A, Baek S, Sung MH, John S, Stixova L, Tesikova M, Hakim O, Miranda T, Hawkins M, Stamatoyannopoulos JA, Chow CC, Hager GL.

Genome Res. 2015 Jun;25(6):845-57. doi: 10.1101/gr.184168.114. Epub 2015 Feb 12.

17.

Genomic discovery of potent chromatin insulators for human gene therapy.

Liu M, Maurano MT, Wang H, Qi H, Song CZ, Navas PA, Emery DW, Stamatoyannopoulos JA, Stamatoyannopoulos G.

Nat Biotechnol. 2015 Feb;33(2):198-203. doi: 10.1038/nbt.3062. Epub 2015 Jan 12.

PMID:
25580597
18.

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution.

Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R, Thurman RE, Johnson AK, Vong S, Lee K, Bates D, Neri F, Diegel M, Giste E, Haugen E, Dunn D, Wilken MS, Josefowicz S, Samstein R, Chang KH, Eichler EE, De Bruijn M, Reh TA, Skoultchi A, Rudensky A, Orkin SH, Papayannopoulou T, Treuting PM, Selleri L, Kaul R, Groudine M, Bender MA, Stamatoyannopoulos JA.

Science. 2014 Nov 21;346(6212):1007-12. doi: 10.1126/science.1246426.

19.

Topologically associating domains are stable units of replication-timing regulation.

Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM.

Nature. 2014 Nov 20;515(7527):402-5. doi: 10.1038/nature13986.

20.

Conservation of trans-acting circuitry during mammalian regulatory evolution.

Stergachis AB, Neph S, Sandstrom R, Haugen E, Reynolds AP, Zhang M, Byron R, Canfield T, Stelhing-Sun S, Lee K, Thurman RE, Vong S, Bates D, Neri F, Diegel M, Giste E, Dunn D, Vierstra J, Hansen RS, Johnson AK, Sabo PJ, Wilken MS, Reh TA, Treuting PM, Kaul R, Groudine M, Bender MA, Borenstein E, Stamatoyannopoulos JA.

Nature. 2014 Nov 20;515(7527):365-70. doi: 10.1038/nature13972.

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