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Results: 1 to 20 of 27

1.

Nuclease-assisted suppression of human DNA background in sepsis.

Song Y, Giske CG, Gille-Johnson P, Emanuelsson O, Lundeberg J, Gyarmati P.

PLoS One. 2014 Jul 30;9(7):e103610. doi: 10.1371/journal.pone.0103610. eCollection 2014.

PMID:
25076135
[PubMed - in process]
Free PMC Article
2.

Analysis of stranded information using an automated procedure for strand specific RNA sequencing.

Sigurgeirsson B, Emanuelsson O, Lundeberg J.

BMC Genomics. 2014 Jul 28;15(1):631. [Epub ahead of print]

PMID:
25070246
[PubMed - as supplied by publisher]
Free Article
3.

Sequencing degraded RNA addressed by 3' tag counting.

Sigurgeirsson B, Emanuelsson O, Lundeberg J.

PLoS One. 2014 Mar 14;9(3):e91851. doi: 10.1371/journal.pone.0091851. eCollection 2014.

PMID:
24632678
[PubMed - in process]
Free PMC Article
4.

The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.

Wiegand S, Meier D, Seehafer C, Malicki M, Hofmann P, Schmith A, Winckler T, Földesi B, Boesler B, Nellen W, Reimegård J, Käller M, Hällman J, Emanuelsson O, Avesson L, Söderbom F, Hammann C.

Nucleic Acids Res. 2014 Mar;42(5):3330-45. doi: 10.1093/nar/gkt1337. Epub 2013 Dec 24.

PMID:
24369430
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Hereditary uveal melanoma: a report of a germline mutation in BAP1.

Höiom V, Edsgärd D, Helgadottir H, Eriksson H, All-Ericsson C, Tuominen R, Ivanova I, Lundeberg J, Emanuelsson O, Hansson J.

Genes Chromosomes Cancer. 2013 Apr;52(4):378-84. doi: 10.1002/gcc.22035. Epub 2013 Jan 23.

PMID:
23341325
[PubMed - indexed for MEDLINE]
6.

Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor.

Uddenberg D, Reimegård J, Clapham D, Almqvist C, von Arnold S, Emanuelsson O, Sundström JF.

Plant Physiol. 2013 Feb;161(2):813-23. doi: 10.1104/pp.112.207746. Epub 2012 Dec 7.

PMID:
23221834
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response.

Iglesias MJ, Reilly SJ, Emanuelsson O, Sennblad B, Pirmoradian Najafabadi M, Folkersen L, Mälarstig A, Lagergren J, Eriksson P, Hamsten A, Odeberg J.

PLoS One. 2012;7(2):e32306. doi: 10.1371/journal.pone.0032306. Epub 2012 Feb 27. Erratum in: PLoS One. 2012;7(4): doi/10.1371/annotation/689ae222-9eb1-4f80-8ebe-6b80e8ad45ce. Jesus Iglesias, Maria [corrected to Iglesias, Maria Jesus].

PMID:
22384210
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

Klevebring D, Fagerberg L, Lundberg E, Emanuelsson O, Uhlén M, Lundeberg J.

BMC Genomics. 2010 Dec 2;11:684. doi: 10.1186/1471-2164-11-684.

PMID:
21126332
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.

Klevebring D, Bjursell M, Emanuelsson O, Lundeberg J.

PLoS One. 2010 Mar 25;5(3):e9762. doi: 10.1371/journal.pone.0009762.

PMID:
20360838
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Sorting signals, N-terminal modifications and abundance of the chloroplast proteome.

Zybailov B, Rutschow H, Friso G, Rudella A, Emanuelsson O, Sun Q, van Wijk KJ.

PLoS One. 2008 Apr 23;3(4):e1994. doi: 10.1371/journal.pone.0001994.

PMID:
18431481
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
17571346
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
17568005
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

What is a gene, post-ENCODE? History and updated definition.

Gerstein MB, Bruce C, Rozowsky JS, Zheng D, Du J, Korbel JO, Emanuelsson O, Zhang ZD, Weissman S, Snyder M.

Genome Res. 2007 Jun;17(6):669-81. Review.

PMID:
17567988
[PubMed - indexed for MEDLINE]
Free Article
14.

Locating proteins in the cell using TargetP, SignalP and related tools.

Emanuelsson O, Brunak S, von Heijne G, Nielsen H.

Nat Protoc. 2007;2(4):953-71.

PMID:
17446895
[PubMed - indexed for MEDLINE]
15.

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.

Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, Gerstein MB.

Genome Res. 2007 Jun;17(6):886-97. Epub 2006 Nov 21.

PMID:
17119069
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Extrapolating traditional DNA microarray statistics to tiling and protein microarray technologies.

Royce TE, Rozowsky JS, Luscombe NM, Emanuelsson O, Yu H, Zhu X, Snyder M, Gerstein MB.

Methods Enzymol. 2006;411:282-311. Review.

PMID:
16939796
[PubMed - indexed for MEDLINE]
17.

Design optimization methods for genomic DNA tiling arrays.

Bertone P, Trifonov V, Rozowsky JS, Schubert F, Emanuelsson O, Karro J, Kao MY, Snyder M, Gerstein M.

Genome Res. 2006 Feb;16(2):271-81. Epub 2005 Dec 19.

PMID:
16365382
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

DNA replication-timing analysis of human chromosome 22 at high resolution and different developmental states.

White EJ, Emanuelsson O, Scalzo D, Royce T, Kosak S, Oakeley EJ, Weissman S, Gerstein M, Groudine M, Snyder M, Schübeler D.

Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17771-6. Epub 2004 Dec 10.

PMID:
15591350
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Analysis of curated and predicted plastid subproteomes of Arabidopsis. Subcellular compartmentalization leads to distinctive proteome properties.

Sun Q, Emanuelsson O, van Wijk KJ.

Plant Physiol. 2004 Jun;135(2):723-34.

PMID:
15208420
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

LumenP--a neural network predictor for protein localization in the thylakoid lumen.

Westerlund I, Von Heijne G, Emanuelsson O.

Protein Sci. 2003 Oct;12(10):2360-6.

PMID:
14500894
[PubMed - indexed for MEDLINE]
Free PMC Article

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