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Items: 1 to 20 of 110

1.

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes.

Macaulay IC, Haerty W, Kumar P, Li YI, Hu TX, Teng MJ, Goolam M, Saurat N, Coupland P, Shirley LM, Smith M, Van der Aa N, Banerjee R, Ellis PD, Quail MA, Swerdlow HP, Zernicka-Goetz M, Livesey FJ, Ponting CP, Voet T.

Nat Methods. 2015 Jun;12(6):519-22. doi: 10.1038/nmeth.3370. Epub 2015 Apr 27.

PMID:
25915121
2.

Epigenetic regulation of COL15A1 in smooth muscle cell replicative aging and atherosclerosis.

Connelly JJ, Cherepanova OA, Doss JF, Karaoli T, Lillard TS, Markunas CA, Nelson S, Wang T, Ellis PD, Langford CF, Haynes C, Seo DM, Goldschmidt-Clermont PJ, Shah SH, Kraus WE, Hauser ER, Gregory SG.

Hum Mol Genet. 2013 Dec 20;22(25):5107-20. doi: 10.1093/hmg/ddt365. Epub 2013 Aug 2.

3.

CCR4-associated factor 1 coordinates the expression of Plasmodium falciparum egress and invasion proteins.

Balu B, Maher SP, Pance A, Chauhan C, Naumov AV, Andrews RM, Ellis PD, Khan SM, Lin JW, Janse CJ, Rayner JC, Adams JH.

Eukaryot Cell. 2011 Sep;10(9):1257-63. doi: 10.1128/EC.05099-11. Epub 2011 Jul 29.

4.

Solid-state (55)Mn NMR spectroscopy of bis(μ-oxo)dimanganese(IV) [Mn(2)O(2)(salpn)(2)], a model for the oxygen evolving complex in photosystem II.

Ellis PD, Sears JA, Yang P, Dupuis M, Boron TT 3rd, Pecoraro VL, Stich TA, Britt RD, Lipton AS.

J Am Chem Soc. 2010 Dec 1;132(47):16727-9. doi: 10.1021/ja1054252. Epub 2010 Nov 8.

PMID:
21058720
5.

Genomic approaches uncover increasing complexities in the regulatory landscape at the human SCL (TAL1) locus.

Dhami P, Bruce AW, Jim JH, Dillon SC, Hall A, Cooper JL, Bonhoure N, Chiang K, Ellis PD, Langford C, Andrews RM, Vetrie D.

PLoS One. 2010 Feb 5;5(2):e9059. doi: 10.1371/journal.pone.0009059.

6.

FRT-seq: amplification-free, strand-specific transcriptome sequencing.

Mamanova L, Andrews RM, James KD, Sheridan EM, Ellis PD, Langford CF, Ost TW, Collins JE, Turner DJ.

Nat Methods. 2010 Feb;7(2):130-2. doi: 10.1038/nmeth.1417. Epub 2010 Jan 17.

7.

Molecular analysis of tumor-promoting CD8+ T cells in two-stage cutaneous chemical carcinogenesis.

Kwong BY, Roberts SJ, Silberzahn T, Filler RB, Neustadter JH, Galan A, Reddy S, Lin WM, Ellis PD, Langford CF, Hayday AC, Girardi M.

J Invest Dermatol. 2010 Jun;130(6):1726-36. doi: 10.1038/jid.2009.362. Epub 2009 Nov 19.

8.

High-field QCPMG NMR of large quadrupolar patterns using resistive magnets.

Hung I, Shetty K, Ellis PD, Brey WW, Gan Z.

Solid State Nucl Magn Reson. 2009 Dec;36(4):159-63. doi: 10.1016/j.ssnmr.2009.10.001. Epub 2009 Oct 30.

PMID:
19913391
9.

Low temperature 65Cu NMR spectroscopy of the Cu+ site in azurin.

Lipton AS, Heck RW, de Jong WA, Gao AR, Wu X, Roehrich A, Harbison GS, Ellis PD.

J Am Chem Soc. 2009 Oct 7;131(39):13992-9. doi: 10.1021/ja901308v.

10.

CARM1 is required in embryonic stem cells to maintain pluripotency and resist differentiation.

Wu Q, Bruce AW, Jedrusik A, Ellis PD, Andrews RM, Langford CF, Glover DM, Zernicka-Goetz M.

Stem Cells. 2009 Nov;27(11):2637-2645. doi: 10.1002/stem.131.

11.

A HaemAtlas: characterizing gene expression in differentiated human blood cells.

Watkins NA, Gusnanto A, de Bono B, De S, Miranda-Saavedra D, Hardie DL, Angenent WG, Attwood AP, Ellis PD, Erber W, Foad NS, Garner SF, Isacke CM, Jolley J, Koch K, Macaulay IC, Morley SL, Rendon A, Rice KM, Taylor N, Thijssen-Timmer DC, Tijssen MR, van der Schoot CE, Wernisch L, Winzer T, Dudbridge F, Buckley CD, Langford CF, Teichmann S, Göttgens B, Ouwehand WH; Bloodomics Consortium.

Blood. 2009 May 7;113(19):e1-9. doi: 10.1182/blood-2008-06-162958. Epub 2009 Feb 19.

12.

Residue ionization in LpxC directly observed by 67Zn NMR spectroscopy.

Lipton AS, Heck RW, Hernick M, Fierke CA, Ellis PD.

J Am Chem Soc. 2008 Sep 24;130(38):12671-9. doi: 10.1021/ja801776c. Epub 2008 Aug 30.

13.

Characterization of Mg2+ binding to the DNA repair protein apurinic/apyrimidic endonuclease 1 via solid-state 25Mg NMR spectroscopy.

Lipton AS, Heck RW, Primak S, McNeill DR, Wilson DM 3rd, Ellis PD.

J Am Chem Soc. 2008 Jul 23;130(29):9332-41. doi: 10.1021/ja0776881. Epub 2008 Jun 25.

14.

67Zn solid-state NMR spectroscopy of ([Tp But,Me]Zn(OH2))[HOB(C6F5)3]. the importance of the anion [HOB(C6F5)3]-.

Lipton AS, Morlok MM, Parkin G, Ellis PD.

Inorg Chem. 2008 Jun 16;47(12):5184-9. doi: 10.1021/ic800009b. Epub 2008 May 10.

PMID:
18470984
15.

A QM/MM approach to interpreting 67Zn solid-state NMR data in zinc proteins.

Lipton AS, Heck RW, Staeheli GR, Valiev M, De Jong WA, Ellis PD.

J Am Chem Soc. 2008 May 14;130(19):6224-30. doi: 10.1021/ja711240t. Epub 2008 Apr 15.

PMID:
18410102
16.

Molecular structure and dynamics in the low temperature (orthorhombic) phase of NH3BH3.

Cho H, Shaw WJ, Parvanov V, Schenter GK, Karkamkar A, Hess NJ, Mundy C, Kathmann S, Sears J, Lipton AS, Ellis PD, Autrey ST.

J Phys Chem A. 2008 May 8;112(18):4277-83. doi: 10.1021/jp7117696. Epub 2008 Apr 12.

PMID:
18407708
17.

Modeling the metal center of Cys4 zinc proteins.

Lipton AS, Ellis PD.

J Am Chem Soc. 2007 Jul 25;129(29):9192-200. Epub 2007 Jun 27.

PMID:
17595082
18.

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.

19.

Butyrate mediates decrease of histone acetylation centered on transcription start sites and down-regulation of associated genes.

Rada-Iglesias A, Enroth S, Ameur A, Koch CM, Clelland GK, Respuela-Alonso P, Wilcox S, Dovey OM, Ellis PD, Langford CF, Dunham I, Komorowski J, Wadelius C.

Genome Res. 2007 Jun;17(6):708-19.

20.

The landscape of histone modifications across 1% of the human genome in five human cell lines.

Koch CM, Andrews RM, Flicek P, Dillon SC, Karaöz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I.

Genome Res. 2007 Jun;17(6):691-707.

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