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Items: 26

1.

Comprehensive RNA-Sequencing Analysis in Serum and Muscle Reveals Novel Small RNA Signatures with Biomarker Potential for DMD.

Coenen-Stass AML, Sork H, Gatto S, Godfrey C, Bhomra A, Krjutškov K, Hart JR, Westholm JO, O'Donovan L, Roos A, Lochmüller H, Puri PL, El Andaloussi S, Wood MJA, Roberts TC.

Mol Ther Nucleic Acids. 2018 Aug 17;13:1-15. doi: 10.1016/j.omtn.2018.08.005. [Epub ahead of print]

2.

Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans.

Cedernaes J, Schönke M, Westholm JO, Mi J, Chibalin A, Voisin S, Osler M, Vogel H, Hörnaeus K, Dickson SL, Lind SB, Bergquist J, Schiöth HB, Zierath JR, Benedict C.

Sci Adv. 2018 Aug 22;4(8):eaar8590. doi: 10.1126/sciadv.aar8590. eCollection 2018 Aug.

3.

Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome.

Sork H, Corso G, Krjutskov K, Johansson HJ, Nordin JZ, Wiklander OPB, Lee YXF, Westholm JO, Lehtiö J, Wood MJA, Mäger I, El Andaloussi S.

Sci Rep. 2018 Jul 17;8(1):10813. doi: 10.1038/s41598-018-28485-9.

4.

Genome-wide identification of Grainy head targets in Drosophila reveals regulatory interactions with the POU domain transcription factor Vvl.

Yao L, Wang S, Westholm JO, Dai Q, Matsuda R, Hosono C, Bray S, Lai EC, Samakovlis C.

Development. 2017 Sep 1;144(17):3145-3155. doi: 10.1242/dev.143297. Epub 2017 Jul 31.

5.

Massive and parallel expression profiling using microarrayed single-cell sequencing.

Vickovic S, Ståhl PL, Salmén F, Giatrellis S, Westholm JO, Mollbrink A, Navarro JF, Custodio J, Bienko M, Sutton LA, Rosenquist R, Frisén J, Lundeberg J.

Nat Commun. 2016 Oct 14;7:13182. doi: 10.1038/ncomms13182.

6.

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J.

Science. 2016 Jul 1;353(6294):78-82. doi: 10.1126/science.aaf2403.

7.

Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family.

Dai Q, Ren A, Westholm JO, Duan H, Patel DJ, Lai EC.

Genes Dev. 2015 Jan 1;29(1):48-62. doi: 10.1101/gad.252122.114.

8.

Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation.

Westholm JO, Miura P, Olson S, Shenker S, Joseph B, Sanfilippo P, Celniker SE, Graveley BR, Lai EC.

Cell Rep. 2014 Dec 11;9(5):1966-1980. doi: 10.1016/j.celrep.2014.10.062. Epub 2014 Nov 26.

9.

Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines.

Wen J, Mohammed J, Bortolamiol-Becet D, Tsai H, Robine N, Westholm JO, Ladewig E, Dai Q, Okamura K, Flynt AS, Zhang D, Andrews J, Cherbas L, Kaufman TC, Cherbas P, Siepel A, Lai EC.

Genome Res. 2014 Jul;24(7):1236-50. doi: 10.1101/gr.161554.113.

10.

Intertwined pathways for Argonaute-mediated microRNA biogenesis in Drosophila.

Yang JS, Smibert P, Westholm JO, Jee D, Maurin T, Lai EC.

Nucleic Acids Res. 2014 Feb;42(3):1987-2002. doi: 10.1093/nar/gkt1038. Epub 2013 Nov 12.

11.

Widespread and extensive lengthening of 3' UTRs in the mammalian brain.

Miura P, Shenker S, Andreu-Agullo C, Westholm JO, Lai EC.

Genome Res. 2013 May;23(5):812-25. doi: 10.1101/gr.146886.112. Epub 2013 Mar 21.

12.

The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors.

Dai Q, Ren A, Westholm JO, Serganov AA, Patel DJ, Lai EC.

Genes Dev. 2013 Mar 15;27(6):602-14. doi: 10.1101/gad.213314.113. Epub 2013 Mar 6.

13.

Discovery of hundreds of mirtrons in mouse and human small RNA data.

Ladewig E, Okamura K, Flynt AS, Westholm JO, Lai EC.

Genome Res. 2012 Sep;22(9):1634-45. doi: 10.1101/gr.133553.111.

14.

Global patterns of tissue-specific alternative polyadenylation in Drosophila.

Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown JB, Eisman RC, Andrews J, Kaufman T, Cherbas P, Celniker SE, Graveley BR, Lai EC.

Cell Rep. 2012 Mar 29;1(3):277-89. Erratum in: Cell Rep. 2013 Mar 28;3(3):969.

15.

Neurophysiological defects and neuronal gene deregulation in Drosophila mir-124 mutants.

Sun K, Westholm JO, Tsurudome K, Hagen JW, Lu Y, Kohwi M, Betel D, Gao FB, Haghighi AP, Doe CQ, Lai EC.

PLoS Genet. 2012 Feb;8(2):e1002515. doi: 10.1371/journal.pgen.1002515. Epub 2012 Feb 9.

16.

Common and distinct patterns of terminal modifications to mirtrons and canonical microRNAs.

Westholm JO, Ladewig E, Okamura K, Robine N, Lai EC.

RNA. 2012 Feb;18(2):177-92. doi: 10.1261/rna.030627.111. Epub 2011 Dec 21.

17.

Histone modifications influence mediator interactions with chromatin.

Zhu X, Zhang Y, Bjornsdottir G, Liu Z, Quan A, Costanzo M, Dávila López M, Westholm JO, Ronne H, Boone C, Gustafsson CM, Myers LC.

Nucleic Acids Res. 2011 Oct;39(19):8342-54. doi: 10.1093/nar/gkr551. Epub 2011 Jul 8.

18.

Mirtrons: microRNA biogenesis via splicing.

Westholm JO, Lai EC.

Biochimie. 2011 Nov;93(11):1897-904. doi: 10.1016/j.biochi.2011.06.017. Epub 2011 Jun 21. Review.

19.

Vive la différence: biogenesis and evolution of microRNAs in plants and animals.

Axtell MJ, Westholm JO, Lai EC.

Genome Biol. 2011;12(4):221. doi: 10.1186/gb-2011-12-4-221. Epub 2011 Apr 28. Review.

20.

Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence.

Berezikov E, Robine N, Samsonova A, Westholm JO, Naqvi A, Hung JH, Okamura K, Dai Q, Bortolamiol-Becet D, Martin R, Zhao Y, Zamore PD, Hannon GJ, Marra MA, Weng Z, Perrimon N, Lai EC.

Genome Res. 2011 Feb;21(2):203-15. doi: 10.1101/gr.116657.110. Epub 2010 Dec 22.

21.

Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans.

Chung WJ, Agius P, Westholm JO, Chen M, Okamura K, Robine N, Leslie CS, Lai EC.

Genome Res. 2011 Feb;21(2):286-300. doi: 10.1101/gr.113050.110. Epub 2010 Dec 22.

22.

Transcriptional profiling reveals a critical role for tyrosine phosphatase VE-PTP in regulation of VEGFR2 activity and endothelial cell morphogenesis.

Mellberg S, Dimberg A, Bahram F, Hayashi M, Rennel E, Ameur A, Westholm JO, Larsson E, Lindahl P, Cross MJ, Claesson-Welsh L.

FASEB J. 2009 May;23(5):1490-502. doi: 10.1096/fj.08-123810. Epub 2009 Jan 9.

PMID:
19136612
23.

Combinatorial control of gene expression by the three yeast repressors Mig1, Mig2 and Mig3.

Westholm JO, Nordberg N, Murén E, Ameur A, Komorowski J, Ronne H.

BMC Genomics. 2008 Dec 16;9:601. doi: 10.1186/1471-2164-9-601.

24.

Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.

Westholm JO, Xu F, Ronne H, Komorowski J.

BMC Bioinformatics. 2008 Nov 17;9:484. doi: 10.1186/1471-2105-9-484.

25.

Endocan is a VEGF-A and PI3K regulated gene with increased expression in human renal cancer.

Rennel E, Mellberg S, Dimberg A, Petersson L, Botling J, Ameur A, Westholm JO, Komorowski J, Lassalle P, Cross MJ, Gerwins P.

Exp Cell Res. 2007 Apr 15;313(7):1285-94. Epub 2007 Feb 6.

PMID:
17362927
26.

Global gene expression analysis by combinatorial optimization.

Ameur A, Aurell E, Carlsson M, Westholm JO.

In Silico Biol. 2004;4(2):225-41.

PMID:
15107026

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