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Items: 44

1.

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells.

Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X.

Nucleic Acids Res. 2017 Jun 2;45(10):e77. doi: 10.1093/nar/gkx026.

2.

Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors.

Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM.

Nucleic Acids Res. 2017 Feb 17;45(3):1281-1296. doi: 10.1093/nar/gkw1214.

3.

Individual heritable differences result in unique cell lymphocyte receptor repertoires of naïve and antigen-experienced cells.

Rubelt F, Bolen CR, McGuire HM, Vander Heiden JA, Gadala-Maria D, Levin M, Euskirchen GM, Mamedov MR, Swan GE, Dekker CL, Cowell LG, Kleinstein SH, Davis MM.

Nat Commun. 2016 Mar 23;7:11112. doi: 10.1038/ncomms11112.

4.

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, Steinmetz LM, Kundaje A, Snyder M.

Cell. 2015 Aug 27;162(5):1051-65. doi: 10.1016/j.cell.2015.07.048. Epub 2015 Aug 20.

5.

Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming.

Tanaka Y, Hysolli E, Su J, Xiang Y, Kim KY, Zhong M, Li Y, Heydari K, Euskirchen G, Snyder MP, Pan X, Weissman SM, Park IH.

Stem Cell Reports. 2015 Jun 9;4(6):1125-39. doi: 10.1016/j.stemcr.2015.04.009. Epub 2015 May 21.

6.

Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.

Li J, Shi M, Ma Z, Zhao S, Euskirchen G, Ziskin J, Urban A, Hallmayer J, Snyder M.

Mol Syst Biol. 2014 Dec 30;10:774. doi: 10.15252/msb.20145487.

7.

Principles of regulatory information conservation between mouse and human.

Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, Yang X, Patacsil D, Keller CA, Giardine B; mouse ENCODE Consortium, Kundaje A, Wang T, Pennacchio LA, Weng Z, Hardison RC, Snyder MP.

Nature. 2014 Nov 20;515(7527):371-375. doi: 10.1038/nature13985.

8.

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.

9.

Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females.

Poznik GD, Henn BM, Yee MC, Sliwerska E, Euskirchen GM, Lin AA, Snyder M, Quintana-Murci L, Kidd JM, Underhill PA, Bustamante CD.

Science. 2013 Aug 2;341(6145):562-5. doi: 10.1126/science.1237619.

10.

Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration.

Zhang Y, Schulz VP, Reed BD, Wang Z, Pan X, Mariani J, Euskirchen G, Snyder MP, Vaccarino FM, Ivanova N, Weissman SM, Szekely AM.

Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12361-6. doi: 10.1073/pnas.1309725110. Epub 2013 Jul 8.

11.

Whole-exome sequencing identifies tetratricopeptide repeat domain 7A (TTC7A) mutations for combined immunodeficiency with intestinal atresias.

Chen R, Giliani S, Lanzi G, Mias GI, Lonardi S, Dobbs K, Manis J, Im H, Gallagher JE, Phanstiel DH, Euskirchen G, Lacroute P, Bettinger K, Moratto D, Weinacht K, Montin D, Gallo E, Mangili G, Porta F, Notarangelo LD, Pedretti S, Al-Herz W, Alfahdli W, Comeau AM, Traister RS, Pai SY, Carella G, Facchetti F, Nadeau KC, Snyder M, Notarangelo LD.

J Allergy Clin Immunol. 2013 Sep;132(3):656-664.e17. doi: 10.1016/j.jaci.2013.06.013. Epub 2013 Jul 4.

12.

Two methods for full-length RNA sequencing for low quantities of cells and single cells.

Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, Lamotte RH, Park IH, Snyder MP, Mason CE, Weissman SM.

Proc Natl Acad Sci U S A. 2013 Jan 8;110(2):594-9. doi: 10.1073/pnas.1217322109. Epub 2012 Dec 24.

13.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

14.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

15.

SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions.

Euskirchen G, Auerbach RK, Snyder M.

J Biol Chem. 2012 Sep 7;287(37):30897-905. doi: 10.1074/jbc.R111.309302. Epub 2012 Sep 5. Review.

16.

Personal omics profiling reveals dynamic molecular and medical phenotypes.

Chen R, Mias GI, Li-Pook-Than J, Jiang L, Lam HY, Chen R, Miriami E, Karczewski KJ, Hariharan M, Dewey FE, Cheng Y, Clark MJ, Im H, Habegger L, Balasubramanian S, O'Huallachain M, Dudley JT, Hillenmeyer S, Haraksingh R, Sharon D, Euskirchen G, Lacroute P, Bettinger K, Boyle AP, Kasowski M, Grubert F, Seki S, Garcia M, Whirl-Carrillo M, Gallardo M, Blasco MA, Greenberg PL, Snyder P, Klein TE, Altman RB, Butte AJ, Ashley EA, Gerstein M, Nadeau KC, Tang H, Snyder M.

Cell. 2012 Mar 16;148(6):1293-307. doi: 10.1016/j.cell.2012.02.009.

17.

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.

Li G, Ruan X, Auerbach RK, Sandhu KS, Zheng M, Wang P, Poh HM, Goh Y, Lim J, Zhang J, Sim HS, Peh SQ, Mulawadi FH, Ong CT, Orlov YL, Hong S, Zhang Z, Landt S, Raha D, Euskirchen G, Wei CL, Ge W, Wang H, Davis C, Fisher-Aylor KI, Mortazavi A, Gerstein M, Gingeras T, Wold B, Sun Y, Fullwood MJ, Cheung E, Liu E, Sung WK, Snyder M, Ruan Y.

Cell. 2012 Jan 20;148(1-2):84-98. doi: 10.1016/j.cell.2011.12.014.

18.

Performance comparison of exome DNA sequencing technologies.

Clark MJ, Chen R, Lam HY, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M.

Nat Biotechnol. 2011 Sep 25;29(10):908-14. doi: 10.1038/nbt.1975.

19.

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches.

Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M.

PLoS Genet. 2011 Mar;7(3):e1002008. doi: 10.1371/journal.pgen.1002008. Epub 2011 Mar 3.

20.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

21.

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.

Bruno VM, Wang Z, Marjani SL, Euskirchen GM, Martin J, Sherlock G, Snyder M.

Genome Res. 2010 Oct;20(10):1451-8. doi: 10.1101/gr.109553.110. Epub 2010 Sep 1.

22.

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.

Nat Struct Mol Biol. 2010 Aug;17(8):920-3. No abstract available.

23.

Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing.

Camarena L, Bruno V, Euskirchen G, Poggio S, Snyder M.

PLoS Pathog. 2010 Apr 1;6(4):e1000834. doi: 10.1371/journal.ppat.1000834.

24.

X chromosome-wide analyses of genomic DNA methylation states and gene expression in male and female neutrophils.

Yasukochi Y, Maruyama O, Mahajan MC, Padden C, Euskirchen GM, Schulz V, Hirakawa H, Kuhara S, Pan XH, Newburger PE, Snyder M, Weissman SM.

Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3704-9. doi: 10.1073/pnas.0914812107. Epub 2010 Feb 2.

25.

Mapping accessible chromatin regions using Sono-Seq.

Auerbach RK, Euskirchen G, Rozowsky J, Lamarre-Vincent N, Moqtaderi Z, Lefrançois P, Struhl K, Gerstein M, Snyder M.

Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14926-31. doi: 10.1073/pnas.0905443106. Epub 2009 Aug 18.

26.

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K.

Nat Struct Mol Biol. 2009 Aug;16(8):847-52. doi: 10.1038/nsmb.1636. Epub 2009 Jul 20.

27.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37.

28.

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB.

Nat Biotechnol. 2009 Jan;27(1):66-75. doi: 10.1038/nbt.1518. Epub 2009 Jan 4.

29.

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding.

Robertson AG, Bilenky M, Tam A, Zhao Y, Zeng T, Thiessen N, Cezard T, Fejes AP, Wederell ED, Cullum R, Euskirchen G, Krzywinski M, Birol I, Snyder M, Hoodless PA, Hirst M, Marra MA, Jones SJ.

Genome Res. 2008 Dec;18(12):1906-17. doi: 10.1101/gr.078519.108. Epub 2008 Sep 11.

30.

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.

Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS.

Genome Res. 2008 Mar;18(3):393-403. doi: 10.1101/gr.7080508. Epub 2008 Feb 7.

31.

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.

Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M.

Genome Biol. 2008 Jan 3;9(1):R3. doi: 10.1186/gb-2008-9-1-r3.

32.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA; NISC Comparative Sequencing Program; Baylor College of Medicine Human Genome Sequencing Center; Washington University Genome Sequencing Center; Broad Institute; Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature. 2007 Jun 14;447(7146):799-816.

33.

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).

Bhinge AA, Kim J, Euskirchen GM, Snyder M, Iyer VR.

Genome Res. 2007 Jun;17(6):910-6.

34.

Mapping of transcription factor binding regions in mammalian cells by ChIP: comparison of array- and sequencing-based technologies.

Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, Ruan Y, Snyder M.

Genome Res. 2007 Jun;17(6):898-909.

35.

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing.

Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S.

Nat Methods. 2007 Aug;4(8):651-7. Epub 2007 Jun 11.

PMID:
17558387
36.

Identification of novel functional elements in the human genome.

Lian Z, Euskirchen G, Rinn J, Martone R, Bertone P, Hartman S, Royce T, Nelson K, Sayward F, Luscombe N, Yang J, Li JL, Miller P, Urban AE, Gerstein M, Weissman S, Snyder M.

Cold Spring Harb Symp Quant Biol. 2003;68:317-22. No abstract available.

PMID:
15338632
37.

Integrative approaches in molecular medicine.

Euskirchen G.

Pharmacogenomics. 2004 Jun;5(4):357-60. No abstract available.

PMID:
15165172
38.

CREB binds to multiple loci on human chromosome 22.

Euskirchen G, Royce TE, Bertone P, Martone R, Rinn JL, Nelson FK, Sayward F, Luscombe NM, Miller P, Gerstein M, Weissman S, Snyder M.

Mol Cell Biol. 2004 May;24(9):3804-14.

39.

A plethora of sites.

Euskirchen G, Snyder M.

Nat Genet. 2004 Apr;36(4):325-6. No abstract available.

PMID:
15054485
40.

Distribution of NF-kappaB-binding sites across human chromosome 22.

Martone R, Euskirchen G, Bertone P, Hartman S, Royce TE, Luscombe NM, Rinn JL, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M.

Proc Natl Acad Sci U S A. 2003 Oct 14;100(21):12247-52. Epub 2003 Oct 3.

41.

The transcriptional activity of human Chromosome 22.

Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M.

Genes Dev. 2003 Feb 15;17(4):529-40.

43.
44.

Green fluorescent protein as a marker for gene expression.

Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC.

Science. 1994 Feb 11;263(5148):802-5.

PMID:
8303295

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