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Items: 1 to 50 of 134

1.

Integrative detection and analysis of structural variation in cancer genomes.

Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F.

Nat Genet. 2018 Sep 10. doi: 10.1038/s41588-018-0195-8. [Epub ahead of print]

PMID:
30202056
2.

Corrigendum: Positively selected enhancer elements endow osteosarcoma cells with metastatic competence.

Morrow JJ, Bayles I, Funnell APW, Miller TE, Saiakhova A, Lizardo MM, Bartels CF, Kapteijn MY, Hung S, Mendoza A, Dhillon G, Chee DR, Myers JT, Allen F, Gambarotti M, Righi A, DiFeo A, Rubin BP, Huang AY, Meltzer PS, Helman LJ, Picci P, Versteeg HH, Stamatoyannopoulos JA, Khanna C, Scacheri PC.

Nat Med. 2018 Apr 10;24(4):525. doi: 10.1038/nm0418-525c.

PMID:
29634688
3.

Positively selected enhancer elements endow osteosarcoma cells with metastatic competence.

Morrow JJ, Bayles I, Funnell APW, Miller TE, Saiakhova A, Lizardo MM, Bartels CF, Kapteijn MY, Hung S, Mendoza A, Dhillon G, Chee DR, Myers JT, Allen F, Gambarotti M, Righi A, DiFeo A, Rubin BP, Huang AY, Meltzer PS, Helman LJ, Picci P, Versteeg HH, Stamatoyannopoulos JA, Khanna C, Scacheri PC.

Nat Med. 2018 Feb;24(2):176-185. doi: 10.1038/nm.4475. Epub 2018 Jan 15. Erratum in: Nat Med. 2018 Apr 10;24(4):525.

4.

Initial high-resolution microscopic mapping of active and inactive regulatory sequences proves non-random 3D arrangements in chromatin domain clusters.

Cremer M, Schmid VJ, Kraus F, Markaki Y, Hellmann I, Maiser A, Leonhardt H, John S, Stamatoyannopoulos J, Cremer T.

Epigenetics Chromatin. 2017 Aug 7;10(1):39. doi: 10.1186/s13072-017-0146-0.

5.

Genetic origins of the Minoans and Mycenaeans.

Lazaridis I, Mittnik A, Patterson N, Mallick S, Rohland N, Pfrengle S, Furtwängler A, Peltzer A, Posth C, Vasilakis A, McGeorge PJP, Konsolaki-Yannopoulou E, Korres G, Martlew H, Michalodimitrakis M, Özsait M, Özsait N, Papathanasiou A, Richards M, Roodenberg SA, Tzedakis Y, Arnott R, Fernandes DM, Hughey JR, Lotakis DM, Navas PA, Maniatis Y, Stamatoyannopoulos JA, Stewardson K, Stockhammer P, Pinhasi R, Reich D, Krause J, Stamatoyannopoulos G.

Nature. 2017 Aug 10;548(7666):214-218. doi: 10.1038/nature23310. Epub 2017 Aug 2.

6.

A single nucleotide polymorphism of cyclin-dependent kinase inhibitor 1B (p27Kip1) associated with human vein graft failure affects growth of human venous adventitial cells but not smooth muscle cells.

Kenagy RD, Kikuchi S, Chen L, Wijelath ES, Stergachis AB, Stamatoyannopoulos J, Tang GL, Clowes AW, Sobel M.

J Vasc Surg. 2018 Jan;67(1):309-317.e7. doi: 10.1016/j.jvs.2016.12.113. Epub 2017 May 16.

PMID:
28526559
7.

Genetics of the peloponnesean populations and the theory of extinction of the medieval peloponnesean Greeks.

Stamatoyannopoulos G, Bose A, Teodosiadis A, Tsetsos F, Plantinga A, Psatha N, Zogas N, Yannaki E, Zalloua P, Kidd KK, Browning BL, Stamatoyannopoulos J, Paschou P, Drineas P.

Eur J Hum Genet. 2017 May;25(5):637-645. doi: 10.1038/ejhg.2017.18. Epub 2017 Mar 8.

8.

52 Genetic Loci Influencing Myocardial Mass.

van der Harst P, van Setten J, Verweij N, Vogler G, Franke L, Maurano MT, Wang X, Mateo Leach I, Eijgelsheim M, Sotoodehnia N, Hayward C, Sorice R, Meirelles O, Lyytikäinen LP, Polašek O, Tanaka T, Arking DE, Ulivi S, Trompet S, Müller-Nurasyid M, Smith AV, Dörr M, Kerr KF, Magnani JW, Del Greco M F, Zhang W, Nolte IM, Silva CT, Padmanabhan S, Tragante V, Esko T, Abecasis GR, Adriaens ME, Andersen K, Barnett P, Bis JC, Bodmer R, Buckley BM, Campbell H, Cannon MV, Chakravarti A, Chen LY, Delitala A, Devereux RB, Doevendans PA, Dominiczak AF, Ferrucci L, Ford I, Gieger C, Harris TB, Haugen E, Heinig M, Hernandez DG, Hillege HL, Hirschhorn JN, Hofman A, Hubner N, Hwang SJ, Iorio A, Kähönen M, Kellis M, Kolcic I, Kooner IK, Kooner JS, Kors JA, Lakatta EG, Lage K, Launer LJ, Levy D, Lundby A, Macfarlane PW, May D, Meitinger T, Metspalu A, Nappo S, Naitza S, Neph S, Nord AS, Nutile T, Okin PM, Olsen JV, Oostra BA, Penninger JM, Pennacchio LA, Pers TH, Perz S, Peters A, Pinto YM, Pfeufer A, Pilia MG, Pramstaller PP, Prins BP, Raitakari OT, Raychaudhuri S, Rice KM, Rossin EJ, Rotter JI, Schafer S, Schlessinger D, Schmidt CO, Sehmi J, Silljé HHW, Sinagra G, Sinner MF, Slowikowski K, Soliman EZ, Spector TD, Spiering W, Stamatoyannopoulos JA, Stolk RP, Strauch K, Tan ST, Tarasov KV, Trinh B, Uitterlinden AG, van den Boogaard M, van Duijn CM, van Gilst WH, Viikari JS, Visscher PM, Vitart V, Völker U, Waldenberger M, Weichenberger CX, Westra HJ, Wijmenga C, Wolffenbuttel BH, Yang J, Bezzina CR, Munroe PB, Snieder H, Wright AF, Rudan I, Boyer LA, Asselbergs FW, van Veldhuisen DJ, Stricker BH, Psaty BM, Ciullo M, Sanna S, Lehtimäki T, Wilson JF, Bandinelli S, Alonso A, Gasparini P, Jukema JW, Kääb S, Gudnason V, Felix SB, Heckbert SR, de Boer RA, Newton-Cheh C, Hicks AA, Chambers JC, Jamshidi Y, Visel A, Christoffels VM, Isaacs A, Samani NJ, de Bakker PIW.

J Am Coll Cardiol. 2016 Sep 27;68(13):1435-1448. doi: 10.1016/j.jacc.2016.07.729.

9.

Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma.

McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Strunk RC, Weiss ST; CAMP Research Group.

Am J Respir Crit Care Med. 2016 Dec 15;194(12):1465-1474.

10.

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 Jul 25;55(31):8975-8. doi: 10.1002/anie.201603945. Epub 2016 Jun 7.

11.

Patterns of Growth and Decline in Lung Function in Persistent Childhood Asthma.

McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Weiss ST, Strunk RC.

N Engl J Med. 2016 May 12;374(19):1842-1852. doi: 10.1056/NEJMoa1513737.

12.

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.

13.

Connecting the regulatory genome.

Stamatoyannopoulos J.

Nat Genet. 2016 Apr 27;48(5):479-80. doi: 10.1038/ng.3553.

PMID:
27120444
14.

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
15.

Genomic footprinting.

Vierstra J, Stamatoyannopoulos JA.

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

PMID:
26914205
16.

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

Turner TN, Hormozdiari F, Duyzend MH, McClymont SA, Hook PW, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman HA, Zody MC, Nelson BJ, Huddleston J, Sandstrom R, Smith JD, Hanna D, Swanson JM, Faustman EM, Bamshad MJ, Stamatoyannopoulos J, Nickerson DA, McCallion AS, Darnell R, Eichler EE.

Am J Hum Genet. 2016 Jan 7;98(1):58-74. doi: 10.1016/j.ajhg.2015.11.023. Epub 2015 Dec 31.

17.

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.

18.

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
19.

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.

20.

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
21.

APOBEC-Induced Cancer Mutations Are Uniquely Enriched in Early-Replicating, Gene-Dense, and Active Chromatin Regions.

Kazanov MD, Roberts SA, Polak P, Stamatoyannopoulos J, Klimczak LJ, Gordenin DA, Sunyaev SR.

Cell Rep. 2015 Nov 10;13(6):1103-1109. doi: 10.1016/j.celrep.2015.09.077. Epub 2015 Oct 29.

22.

Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution.

He X, Tillo D, Vierstra J, Syed KS, Deng C, Ray GJ, Stamatoyannopoulos J, FitzGerald PC, Vinson C.

Genome Biol Evol. 2015 Oct 27;7(11):3155-69. doi: 10.1093/gbe/evv205.

23.

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.

24.

Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults.

Hochner H, Allard C, Granot-Hershkovitz E, Chen J, Sitlani CM, Sazdovska S, Lumley T, McKnight B, Rice K, Enquobahrie DA, Meigs JB, Kwok P, Hivert MF, Borecki IB, Gomez F, Wang T, van Duijn C, Amin N, Rotter JI, Stamatoyannopoulos J, Meiner V, Manor O, Dupuis J, Friedlander Y, Siscovick DS.

PLoS Genet. 2015 Oct 9;11(10):e1005573. doi: 10.1371/journal.pgen.1005573. eCollection 2015 Oct.

25.

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.

26.

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.

27.

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.

28.

DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements.

Wilken MS, Brzezinski JA, La Torre A, Siebenthall K, Thurman R, Sabo P, Sandstrom RS, Vierstra J, Canfield TK, Hansen RS, Bender MA, Stamatoyannopoulos J, Reh TA.

Epigenetics Chromatin. 2015 Feb 28;8:8. doi: 10.1186/1756-8935-8-8. eCollection 2015.

29.

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):541-554. doi: 10.1016/j.cell.2015.03.010.

30.

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

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

Nature. 2015 Feb 19;518(7539):360-364. doi: 10.1038/nature14221.

31.

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.

32.

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.

33.

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
34.

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.

35.

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.

36.

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.

37.

A comparative encyclopedia of DNA elements in the mouse genome.

Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D, Amrhein H, Fisher-Aylor K, Antoshechkin I, DeSalvo G, See LH, Fastuca M, Drenkow J, Zaleski C, Dobin A, Prieto P, Lagarde J, Bussotti G, Tanzer A, Denas O, Li K, Bender MA, Zhang M, Byron R, Groudine MT, McCleary D, Pham L, Ye Z, Kuan S, Edsall L, Wu YC, Rasmussen MD, Bansal MS, Kellis M, Keller CA, Morrissey CS, Mishra T, Jain D, Dogan N, Harris RS, Cayting P, Kawli T, Boyle AP, Euskirchen G, Kundaje A, Lin S, Lin Y, Jansen C, Malladi VS, Cline MS, Erickson DT, Kirkup VM, Learned K, Sloan CA, Rosenbloom KR, Lacerda de Sousa B, Beal K, Pignatelli M, Flicek P, Lian J, Kahveci T, Lee D, Kent WJ, Ramalho Santos M, Herrero J, Notredame C, Johnson A, Vong S, Lee K, Bates D, Neri F, Diegel M, Canfield T, Sabo PJ, Wilken MS, Reh TA, Giste E, Shafer A, Kutyavin T, Haugen E, Dunn D, Reynolds AP, Neph S, Humbert R, Hansen RS, De Bruijn M, Selleri L, Rudensky A, Josefowicz S, Samstein R, Eichler EE, Orkin SH, Levasseur D, Papayannopoulou T, Chang KH, Skoultchi A, Gosh S, Disteche C, Treuting P, Wang Y, Weiss MJ, Blobel GA, Cao X, Zhong S, Wang T, Good PJ, Lowdon RF, Adams LB, Zhou XQ, Pazin MJ, Feingold EA, Wold B, Taylor J, Mortazavi A, Weissman SM, Stamatoyannopoulos JA, Snyder MP, Guigo R, Gingeras TR, Gilbert DM, Hardison RC, Beer MA, Ren B; Mouse ENCODE Consortium.

Nature. 2014 Nov 20;515(7527):355-64. doi: 10.1038/nature13992.

38.

Resolving the complexity of the human genome using single-molecule sequencing.

Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE.

Nature. 2015 Jan 29;517(7536):608-11. doi: 10.1038/nature13907. Epub 2014 Nov 10.

39.

A genome-wide map of adeno-associated virus-mediated human gene targeting.

Deyle DR, Hansen RS, Cornea AM, Li LB, Burt AA, Alexander IE, Sandstrom RS, Stamatoyannopoulos JA, Wei CL, Russell DW.

Nat Struct Mol Biol. 2014 Nov;21(11):969-75. doi: 10.1038/nsmb.2895. Epub 2014 Oct 5.

40.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Aug 19;111(33):E3366. No abstract available.

41.

Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana.

Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV 3rd, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA.

Cell Rep. 2014 Sep 25;8(6):2015-2030. doi: 10.1016/j.celrep.2014.08.019. Epub 2014 Sep 15.

42.

Maritime route of colonization of Europe.

Paschou P, Drineas P, Yannaki E, Razou A, Kanaki K, Tsetsos F, Padmanabhuni SS, Michalodimitrakis M, Renda MC, Pavlovic S, Anagnostopoulos A, Stamatoyannopoulos JA, Kidd KK, Stamatoyannopoulos G.

Proc Natl Acad Sci U S A. 2014 Jun 24;111(25):9211-6. doi: 10.1073/pnas.1320811111. Epub 2014 Jun 9.

43.

Guidelines for investigating causality of sequence variants in human disease.

MacArthur DG, Manolio TA, Dimmock DP, Rehm HL, Shendure J, Abecasis GR, Adams DR, Altman RB, Antonarakis SE, Ashley EA, Barrett JC, Biesecker LG, Conrad DF, Cooper GM, Cox NJ, Daly MJ, Gerstein MB, Goldstein DB, Hirschhorn JN, Leal SM, Pennacchio LA, Stamatoyannopoulos JA, Sunyaev SR, Valle D, Voight BF, Winckler W, Gunter C.

Nature. 2014 Apr 24;508(7497):469-76. doi: 10.1038/nature13127.

44.

Defining functional DNA elements in the human genome.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A. 2014 Apr 29;111(17):6131-8. doi: 10.1073/pnas.1318948111. Epub 2014 Apr 21. Review.

45.

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. 2014 Apr 17;508(7496):345-50. doi: 10.1038/nature13200. Erratum in: Nature. 2016 Mar 17;531(7594):400.

PMID:
24740065
46.

Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells.

Arvey A, van der Veeken J, Samstein RM, Feng Y, Stamatoyannopoulos JA, Rudensky AY.

Nat Immunol. 2014 Jun;15(6):580-587. doi: 10.1038/ni.2868. Epub 2014 Apr 13.

47.

Exonic transcription factor binding directs codon choice and affects protein evolution.

Stergachis AB, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, Raubitschek A, Ziegler S, LeProust EM, Akey JM, Stamatoyannopoulos JA.

Science. 2013 Dec 13;342(6164):1367-72. doi: 10.1126/science.1243490.

48.

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.

Polak P, Lawrence MS, Haugen E, Stoletzki N, Stojanov P, Thurman RE, Garraway LA, Mirkin S, Getz G, Stamatoyannopoulos JA, Sunyaev SR.

Nat Biotechnol. 2014 Jan;32(1):71-5. doi: 10.1038/nbt.2778. Epub 2013 Dec 15.

49.

Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.

Vierstra J, Wang H, John S, Sandstrom R, Stamatoyannopoulos JA.

Nat Methods. 2014 Jan;11(1):66-72. doi: 10.1038/nmeth.2713. Epub 2013 Nov 3.

PMID:
24185839
50.

Functionally and phenotypically distinct subpopulations of marrow stromal cells are fibroblast in origin and induce different fates in peripheral blood monocytes.

Iwata M, Sandstrom RS, Delrow JJ, Stamatoyannopoulos JA, Torok-Storb B.

Stem Cells Dev. 2014 Apr 1;23(7):729-40. doi: 10.1089/scd.2013.0300. Epub 2013 Nov 23.

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