Publications

January 9th, 2010

There are 43 published papers

 

A conceptual framework for the identification of candidate drugs and drug targets in acute promyelocytic leukemia.

Marstrand TT, Borup R, Willer A, Borregaard N, Sandelin A, Porse BT, Theilgaard-Mönch K.

Leukemia. 2010 Jul;24(7):1265-75. Epub 2010 May 27.PMID: 20508621 [PubMed - in process]Related citations

Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia.

Stephens NA, Gallagher IJ, Rooyackers O, Skipworth RJ, Tan BH, Marstrand T, Ross JA, Guttridge DC, Lundell L, Fearon KC, Timmons JA.

Genome Med. 2010 Jan 15;2(1):1.PMID: 20193046 [PubMed - in process]Free PMC ArticleFree textRelated citations

Ancient human genome sequence of an extinct Palaeo-Eskimo.

Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Grønnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Pontén T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E.

Nature. 2010 Feb 11;463(7282):757-62.PMID: 20148029 [PubMed - indexed for MEDLINE]Related citations

miRMaid: a unified programming interface for microRNA data resources.

Jacobsen A, Krogh A, Kauppinen S, Lindow M.

BMC Bioinformatics. 2010 Jan 14;11:29.PMID: 20074352 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Persistent organic pollutant exposure leads to insulin resistance syndrome.

Ruzzin J, Petersen R, Meugnier E, Madsen L, Lock EJ, Lillefosse H, Ma T, Pesenti S, Sonne SB, Marstrand TT, Malde MK, Du ZY, Chavey C, Fajas L, Lundebye AK, Brand CL, Vidal H, Kristiansen K, Frøyland L.

Environ Health Perspect. 2010 Apr;118(4):465-71. Epub 2009 Nov 19.PMID: 20064776 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection.

Lanford RE, Hildebrandt-Eriksen ES, Petri A, Persson R, Lindow M, Munk ME, Kauppinen S, Ørum H.

Science. 2010 Jan 8;327(5962):198-201. Epub 2009 Dec 3.PMID: 19965718 [PubMed - indexed for MEDLINE]Related citations

De novo prediction of structured RNAs from genomic sequences.

Gorodkin J, Hofacker IL, Torarinsson E, Yao Z, Havgaard JH, Ruzzo WL.

Trends Biotechnol. 2010 Jan;28(1):9-19. Epub 2009 Nov 26. Review.PMID: 19942311 [PubMed - indexed for MEDLINE]Related citations

Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing.

Nygaard S, Jacobsen A, Lindow M, Eriksen J, Balslev E, Flyger H, Tolstrup N, Møller S, Krogh A, Litman T.

BMC Med Genomics. 2009 Jun 9;2:35.PMID: 19508715 [PubMed]Free PMC ArticleFree textRelated citations

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.

FANTOM Consortium, Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Björkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engström PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hörnquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schönbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegnér J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA; Riken Omics Science Center, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y.

Nat Genet. 2009 May;41(5):553-62. Epub 2009 Apr 19.PMID: 19377474 [PubMed - indexed for MEDLINE]Related citations

MicroRNA silencing in primates: towards development of novel therapeutics.

Petri A, Lindow M, Kauppinen S.

Cancer Res. 2009 Jan 15;69(2):393-5. Review.PMID: 19147547 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies.

Anandam P, Torarinsson E, Ruzzo WL.

Bioinformatics. 2009 Mar 1;25(5):668-9. Epub 2009 Jan 9.PMID: 19136551 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE.

Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P.

Genome Res. 2009 Feb;19(2):255-65. Epub 2008 Dec 11.PMID: 19074369 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Structural profiles of human miRNA families from pairwise clustering.

Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J.

Bioinformatics. 2009 Feb 1;25(3):291-4. Epub 2008 Dec 4.PMID: 19059941 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Targeting of microRNAs for therapeutics.

Stenvang J, Lindow M, Kauppinen S.

Biochem Soc Trans. 2008 Dec;36(Pt 6):1197-200.PMID: 19021524 [PubMed - indexed for MEDLINE]Related citations

Rfam: updates to the RNA families database.

Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A.

Nucleic Acids Res. 2009 Jan;37(Database issue):D136-40. Epub 2008 Oct 25.PMID: 18953034 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140.

Nicolas FE, Pais H, Schwach F, Lindow M, Kauppinen S, Moulton V, Dalmay T.

RNA. 2008 Dec;14(12):2513-20. Epub 2008 Oct 22.PMID: 18945805 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Modeling promoter grammars with evolving hidden Markov models.

Won KJ, Sandelin A, Marstrand TT, Krogh A.

Bioinformatics. 2008 Aug 1;24(15):1669-75. Epub 2008 Jun 5.PMID: 18535083 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

WAR: Webserver for aligning structural RNAs.

Torarinsson E, Lindgreen S.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W79-84. Epub 2008 May 20.PMID: 18492721 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

LNA-mediated microRNA silencing in non-human primates.

Elmén J, Lindow M, Schütz S, Lawrence M, Petri A, Obad S, Lindholm M, Hedtjärn M, Hansen HF, Berger U, Gullans S, Kearney P, Sarnow P, Straarup EM, Kauppinen S.

Nature. 2008 Apr 17;452(7189):896-9. Epub 2008 Mar 26.PMID: 18368051 [PubMed - indexed for MEDLINE]Related citations

The utility of LNA in microRNA-based cancer diagnostics and therapeutics.

Stenvang J, Silahtaroglu AN, Lindow M, Elmen J, Kauppinen S.

Semin Cancer Biol. 2008 Apr;18(2):89-102. Epub 2008 Jan 15. Review.PMID: 18295505 [PubMed - indexed for MEDLINE]Related citations

Asap: a framework for over-representation statistics for transcription factor binding sites.

Marstrand TT, Frellsen J, Moltke I, Thiim M, Valen E, Retelska D, Krogh A.

PLoS One. 2008 Feb 20;3(2):e1623.PMID: 18286180 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

The genome landscape of ERalpha- and ERbeta-binding DNA regions.

Liu Y, Gao H, Marstrand TT, Ström A, Valen E, Sandelin A, Gustafsson JA, Dahlman-Wright K.

Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2604-9. Epub 2008 Feb 13.PMID: 18272478 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver.

Elmén J, Lindow M, Silahtaroglu A, Bak M, Christensen M, Lind-Thomsen A, Hedtjärn M, Hansen JB, Hansen HF, Straarup EM, McCullagh K, Kearney P, Kauppinen S.

Nucleic Acids Res. 2008 Mar;36(4):1153-62. Epub 2007 Dec 23.PMID: 18158304 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions.

Torarinsson E, Yao Z, Wiklund ED, Bramsen JB, Hansen C, Kjems J, Tommerup N, Ruzzo WL, Gorodkin J.

Genome Res. 2008 Feb;18(2):242-51. Epub 2007 Dec 20.PMID: 18096747 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants.

Lindow M, Jacobsen A, Nygaard S, Mang Y, Krogh A.

PLoS Comput Biol. 2007 Nov;3(11):e238.PMID: 18052543 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Cholecystokinin-2 receptor mediated gene expression in neuronal PC12 cells.

Hansen TO, Borup R, Marstrand T, Rehfeld JF, Nielsen FC.

J Neurochem. 2008 Mar;104(6):1450-65. Epub 2007 Nov 17.PMID: 18028338 [PubMed - indexed for MEDLINE]Related citations

JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A.

Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6. Epub 2007 Nov 15.PMID: 18006571 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.

Lindgreen S, Gardner PP, Krogh A.

Bioinformatics. 2007 Dec 15;23(24):3304-11. Epub 2007 Nov 15.PMID: 18006551 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells.

Frankel LB, Christoffersen NR, Jacobsen A, Lindow M, Krogh A, Lund AH.

J Biol Chem. 2008 Jan 11;283(2):1026-33. Epub 2007 Nov 8.PMID: 17991735 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix.

Havgaard JH, Torarinsson E, Gorodkin J.

PLoS Comput Biol. 2007 Oct;3(10):1896-908. Epub 2007 Aug 20.PMID: 17937495 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Brain expressed microRNAs implicated in schizophrenia etiology.

Hansen T, Olsen L, Lindow M, Jakobsen KD, Ullum H, Jonsson E, Andreassen OA, Djurovic S, Melle I, Agartz I, Hall H, Timm S, Wang AG, Werge T.

PLoS One. 2007 Sep 12;2(9):e873.PMID: 17849003 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Semiautomated improvement of RNA alignments.

Andersen ES, Lind-Thomsen A, Knudsen B, Kristensen SE, Havgaard JH, Torarinsson E, Larsen N, Zwieb C, Sestoft P, Kjems J, Gorodkin J.

RNA. 2007 Nov;13(11):1850-9. Epub 2007 Sep 5.PMID: 17804647 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Principles and limitations of computational microRNA gene and target finding.

Lindow M, Gorodkin J.

DNA Cell Biol. 2007 May;26(5):339-51. Review.PMID: 17504029 [PubMed - indexed for MEDLINE]Related citations

Multiple structural alignment and clustering of RNA sequences.

Torarinsson E, Havgaard JH, Gorodkin J.

Bioinformatics. 2007 Apr 15;23(8):926-32. Epub 2007 Feb 25.PMID: 17324941 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Measuring covariation in RNA alignments: physical realism improves information measures.

Lindgreen S, Gardner PP, Krogh A.

Bioinformatics. 2006 Dec 15;22(24):2988-95. Epub 2006 Oct 12.PMID: 17038338 [PubMed - indexed for MEDLINE]Free ArticleRelated citations

Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure.

Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J.

Genome Res. 2006 Jul;16(7):885-9. Epub 2006 Jun 2. Erratum in: Genome Res. 2006 Nov;16(11):1439. PMID: 16751343 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Computational evidence for hundreds of non-conserved plant microRNAs.

Lindow M, Krogh A.

BMC Genomics. 2005 Sep 13;6:119.PMID: 16159385 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota.

Chen L, Brügger K, Skovgaard M, Redder P, She Q, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA.

J Bacteriol. 2005 Jul;187(14):4992-9.PMID: 15995215 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Divergent transcriptional and translational signals in Archaea.

Torarinsson E, Klenk HP, Garrett RA.

Environ Microbiol. 2005 Jan;7(1):47-54.PMID: 15643935 [PubMed - indexed for MEDLINE]Related citations

Shuffling of Sulfolobus genomes by autonomous and non-autonomous mobile elements.

Brügger K, Torarinsson E, Redder P, Chen L, Garrett RA.

Biochem Soc Trans. 2004 Apr;32(Pt 2):179-83. Review.PMID: 15046567 [PubMed - indexed for MEDLINE]Related citations

The virus-encoded chemokine vMIP-II inhibits virus-induced Tc1-driven inflammation.

Lindow M, Nansen A, Bartholdy C, Stryhn A, Hansen NJ, Boesen TP, Wells TN, Schwartz TW, Thomsen AR.

J Virol. 2003 Jul;77(13):7393-400.PMID: 12805438 [PubMed - indexed for MEDLINE]Free PMC ArticleFree textRelated citations

Viral leads for chemokine-modulatory drugs.

Lindow M, Lüttichau HR, Schwartz TW.

Trends Pharmacol Sci. 2003 Mar;24(3):126-30. Review.PMID: 12628357 [PubMed - indexed for MEDLINE]Related citations

Storage of trachea for X-ray microanalytical studies of tracheal submucosal glands.

Vanthanouvong V, Dragomir A, Lindow M, Roomans GM.

J Submicrosc Cytol Pathol. 1998 Oct;30(4):511-5.PMID: 9851059 [PubMed - indexed for MEDLINE]Related citations

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