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Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases.

Lundmark A, Davanian H, Båge T, Johannsen G, Koro C, Lundeberg J, Yucel-Lindberg T.

Sci Rep. 2015 Dec 21;5:18475. doi: 10.1038/srep18475.


Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.

Bersani C, Huss M, Giacomello S, Xu LD, Bianchi J, Eriksson S, Jerhammar F, Alexeyenko A, Vilborg A, Lundeberg J, Lui WO, Wiman KG.

Oncotarget. 2016 Jan 12;7(2):1895-911. doi: 10.18632/oncotarget.6557.


Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.

Kvastad L, Werne Solnestam B, Johansson E, Nygren AO, Laddach N, Sahlén P, Vickovic S, Bendigtsen SC, Aaserud M, Floer L, Borgen E, Schwind C, Himmelreich R, Latta D, Lundeberg J.

Sci Rep. 2015 Nov 12;5:16519. doi: 10.1038/srep16519.


Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

Delhomme N, Sundström G, Zamani N, Lantz H, Lin YC, Hvidsten TR, Höppner MP, Jern P, Van de Peer Y, Lundeberg J, Grabherr MG, Street NR.

PLoS One. 2015 Sep 28;10(9):e0139080. doi: 10.1371/journal.pone.0139080. eCollection 2015.


Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.

Stödberg T, McTague A, Ruiz AJ, Hirata H, Zhen J, Long P, Farabella I, Meyer E, Kawahara A, Vassallo G, Stivaros SM, Bjursell MK, Stranneheim H, Tigerschiöld S, Persson B, Bangash I, Das K, Hughes D, Lesko N, Lundeberg J, Scott RC, Poduri A, Scheffer IE, Smith H, Gissen P, Schorge S, Reith ME, Topf M, Kullmann DM, Harvey RJ, Wedell A, Kurian MA.

Nat Commun. 2015 Sep 3;6:8038. doi: 10.1038/ncomms9038.


Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.

Sahlén P, Abdullayev I, Ramsköld D, Matskova L, Rilakovic N, Lötstedt B, Albert TJ, Lundeberg J, Sandberg R.

Genome Biol. 2015 Aug 3;16:156. doi: 10.1186/s13059-015-0727-9.


Endonuclease specificity and sequence dependence of type IIS restriction enzymes.

Lundin S, Jemt A, Terje-Hegge F, Foam N, Pettersson E, Käller M, Wirta V, Lexow P, Lundeberg J.

PLoS One. 2015 Jan 28;10(1):e0117059. doi: 10.1371/journal.pone.0117059. eCollection 2015.


The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.

Kutsenko A, Svensson T, Nystedt B, Lundeberg J, Björk P, Sonnhammer E, Giacomello S, Visa N, Wieslander L.

BMC Genomics. 2014 Sep 27;15:819. doi: 10.1186/1471-2164-15-819.


BESST--efficient scaffolding of large fragmented assemblies.

Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L.

BMC Bioinformatics. 2014 Aug 15;15:281. doi: 10.1186/1471-2105-15-281.


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.


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

Sigurgeirsson B, Emanuelsson O, Lundeberg J.

BMC Genomics. 2014 Jul 28;15:631. doi: 10.1186/1471-2164-15-631.


Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.

Alexeyenko A, Nystedt B, Vezzi F, Sherwood E, Ye R, Knudsen B, Simonsen M, Turner B, de Jong P, Wu CC, Lundeberg J.

BMC Genomics. 2014 Jun 6;15:439. doi: 10.1186/1471-2164-15-439.


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.


Assessment of whole genome amplification for sequence capture and massively parallel sequencing.

Hasmats J, Gréen H, Orear C, Validire P, Huss M, Käller M, Lundeberg J.

PLoS One. 2014 Jan 7;9(1):e84785. doi: 10.1371/journal.pone.0084785. eCollection 2014.


Integrated molecular portrait of non-small cell lung cancers.

Lazar V, Suo C, Orear C, van den Oord J, Balogh Z, Guegan J, Job B, Meurice G, Ripoche H, Calza S, Hasmats J, Lundeberg J, Lacroix L, Vielh P, Dufour F, Lehtiö J, Napieralski R, Eggermont A, Schmitt M, Cadranel J, Besse B, Girard P, Blackhall F, Validire P, Soria JC, Dessen P, Hansson J, Pawitan Y.

BMC Med Genomics. 2013 Dec 3;6:53. doi: 10.1186/1755-8794-6-53.


Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.

Lundin S, Gruselius J, Nystedt B, Lexow P, Käller M, Lundeberg J.

Sci Rep. 2013;3:1186. doi: 10.1038/srep01186.


TagGD: fast and accurate software for DNA Tag generation and demultiplexing.

Costea PI, Lundeberg J, Akan P.

PLoS One. 2013;8(3):e57521. doi: 10.1371/journal.pone.0057521. Epub 2013 Mar 4.


Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.

Gioti A, Nystedt B, Li W, Xu J, Andersson A, Averette AF, Münch K, Wang X, Kappauf C, Kingsbury JM, Kraak B, Walker LA, Johansson HJ, Holm T, Lehtiö J, Stajich JE, Mieczkowski P, Kahmann R, Kennell JC, Cardenas ME, Lundeberg J, Saunders CW, Boekhout T, Dawson TL, Munro CA, de Groot PW, Butler G, Heitman J, Scheynius A.

MBio. 2013 Jan 22;4(1):e00572-12. doi: 10.1128/mBio.00572-12.


Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.

Akan P, Alexeyenko A, Costea PI, Hedberg L, Solnestam BW, Lundin S, Hällman J, Lundberg E, Uhlén M, Lundeberg J.

Genome Med. 2012 Nov 18;4(11):86. doi: 10.1186/gm387. eCollection 2012.


Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.

Solnestam BW, Stranneheim H, Hällman J, Käller M, Lundberg E, Lundeberg J, Akan P.

BMC Genomics. 2012 Oct 30;13:574. doi: 10.1186/1471-2164-13-574.

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