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Items: 1 to 50 of 262

1.

Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.

Järver P, Dondalska A, Poux C, Sandberg A, Bergenstråhle J, Sköld AE, Dereuddre-Bosquet N, Martinon F, Pålsson S, Zaghloul E, Brodin D, Sander B, Lennox KA, Behlke MA, El-Andaloussi S, Lehtiö J, Lundeberg J, LeGrand R, Spetz AL.

Sci Rep. 2018 Oct 26;8(1):15841. doi: 10.1038/s41598-018-33960-4.

2.

Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays.

Giacomello S, Lundeberg J.

Nat Protoc. 2018 Nov;13(11):2425-2446. doi: 10.1038/s41596-018-0046-1.

PMID:
30353173
3.

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.

Salmén F, Ståhl PL, Mollbrink A, Navarro JF, Vickovic S, Frisén J, Lundeberg J.

Nat Protoc. 2018 Nov;13(11):2501-2534. doi: 10.1038/s41596-018-0045-2.

PMID:
30353172
4.

Response to Burtscher re: "Increased Cytokines at High Altitude: Lack of Effect of Ibuprofen on Acute Mountain Sickness, Physiological Variables, or Cytokine Levels".

Bickler P, Feiner JR, Lundeberg J.

High Alt Med Biol. 2018 Sep;19(3):304-305. doi: 10.1089/ham.2018.0092. No abstract available.

PMID:
30239230
5.

Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.

Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J.

Cancer Res. 2018 Oct 15;78(20):5970-5979. doi: 10.1158/0008-5472.CAN-18-0747. Epub 2018 Aug 28.

PMID:
30154148
6.

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.

Hu YOO, Ndegwa N, Alneberg J, Johansson S, Logue JB, Huss M, Käller M, Lundeberg J, Fagerberg J, Andersson AF.

Sci Rep. 2018 Aug 9;8(1):11907. doi: 10.1038/s41598-018-29920-7.

7.

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.

Berglund E, Maaskola J, Schultz N, Friedrich S, Marklund M, Bergenstråhle J, Tarish F, Tanoglidi A, Vickovic S, Larsson L, Salmén F, Ogris C, Wallenborg K, Lagergren J, Ståhl P, Sonnhammer E, Helleday T, Lundeberg J.

Nat Commun. 2018 Jun 20;9(1):2419. doi: 10.1038/s41467-018-04724-5.

8.

Increased Cytokines at High Altitude: Lack of Effect of Ibuprofen on Acute Mountain Sickness, Physiological Variables, or Cytokine Levels.

Lundeberg J, Feiner JR, Schober A, Sall JW, Eilers H, Bickler PE.

High Alt Med Biol. 2018 Sep;19(3):249-258. doi: 10.1089/ham.2017.0144. Epub 2018 Jun 20.

PMID:
29924642
9.

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.

Lundmark A, Gerasimcik N, Båge T, Jemt A, Mollbrink A, Salmén F, Lundeberg J, Yucel-Lindberg T.

Sci Rep. 2018 Jun 19;8(1):9370. doi: 10.1038/s41598-018-27627-3.

10.

Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.

Dias DO, Kim H, Holl D, Werne Solnestam B, Lundeberg J, Carlén M, Göritz C, Frisén J.

Cell. 2018 Mar 22;173(1):153-165.e22. doi: 10.1016/j.cell.2018.02.004. Epub 2018 Mar 1.

11.

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets.

Wong K, Navarro JF, Bergenstråhle L, Ståhl PL, Lundeberg J.

Bioinformatics. 2018 Jun 1;34(11):1966-1968. doi: 10.1093/bioinformatics/bty030.

PMID:
29360929
12.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

13.

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.

Asp M, Salmén F, Ståhl PL, Vickovic S, Felldin U, Löfling M, Fernandez Navarro J, Maaskola J, Eriksson MJ, Persson B, Corbascio M, Persson H, Linde C, Lundeberg J.

Sci Rep. 2017 Oct 11;7(1):12941. doi: 10.1038/s41598-017-13462-5.

14.

SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

Ameur A, Dahlberg J, Olason P, Vezzi F, Karlsson R, Martin M, Viklund J, Kähäri AK, Lundin P, Che H, Thutkawkorapin J, Eisfeldt J, Lampa S, Dahlberg M, Hagberg J, Jareborg N, Liljedahl U, Jonasson I, Johansson Å, Feuk L, Lundeberg J, Syvänen AC, Lundin S, Nilsson D, Nystedt B, Magnusson PK, Gyllensten U.

Eur J Hum Genet. 2017 Nov;25(11):1253-1260. doi: 10.1038/ejhg.2017.130. Epub 2017 Aug 23.

15.

Spatially resolved transcriptome profiling in model plant species.

Giacomello S, Salmén F, Terebieniec BK, Vickovic S, Navarro JF, Alexeyenko A, Reimegård J, McKee LS, Mannapperuma C, Bulone V, Ståhl PL, Sundström JF, Street NR, Lundeberg J.

Nat Plants. 2017 May 8;3:17061. doi: 10.1038/nplants.2017.61.

PMID:
28481330
16.

ST Pipeline: an automated pipeline for spatial mapping of unique transcripts.

Navarro JF, Sjöstrand J, Salmén F, Lundeberg J, Ståhl PL.

Bioinformatics. 2017 Aug 15;33(16):2591-2593. doi: 10.1093/bioinformatics/btx211.

PMID:
28398467
17.

Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.

Sigurgeirsson B, Åmark H, Jemt A, Ujvari D, Westgren M, Lundeberg J, Gidlöf S.

Biol Reprod. 2017 Jan 1;96(1):24-33. doi: 10.1095/biolreprod.116.142547.

PMID:
28395321
18.

Corrigendum: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.

Jemt A, Salmén F, Lundmark A, Mollbrink A, Navarro JF, Ståhl PL, Yucel-Lindberg T, Lundeberg J.

Sci Rep. 2017 Mar 13;7:41109. doi: 10.1038/srep41109. No abstract available.

19.

Electrochemical Genetic Profiling of Single Cancer Cells.

Acero Sánchez JL, Joda H, Henry OY, Solnestam BW, Kvastad L, Akan PS, Lundeberg J, Laddach N, Ramakrishnan D, Riley I, Schwind C, Latta D, O'Sullivan CK.

Anal Chem. 2017 Mar 21;89(6):3378-3385. doi: 10.1021/acs.analchem.6b03973. Epub 2017 Feb 28.

PMID:
28211676
20.

Comparison of whole genome amplification techniques for human single cell exome sequencing.

Borgström E, Paterlini M, Mold JE, Frisen J, Lundeberg J.

PLoS One. 2017 Feb 16;12(2):e0171566. doi: 10.1371/journal.pone.0171566. eCollection 2017.

21.

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Zhu Y, Engström PG, Tellgren-Roth C, Baudo CD, Kennell JC, Sun S, Billmyre RB, Schröder MS, Andersson A, Holm T, Sigurgeirsson B, Wu G, Sankaranarayanan SR, Siddharthan R, Sanyal K, Lundeberg J, Nystedt B, Boekhout T, Dawson TL Jr, Heitman J, Scheynius A, Lehtiö J.

Nucleic Acids Res. 2017 Mar 17;45(5):2629-2643. doi: 10.1093/nar/gkx006.

22.

Quality Matters: 2016 Annual Conference of the National Infrastructures for Biobanking.

Doucet M, Becker KF, Björkman J, Bonnet J, Clément B, Daidone MG, Duyckaerts C, Erb G, Haslacher H, Hofman P, Huppertz B, Junot C, Lundeberg J, Metspalu A, Lavitrano M, Litton JE, Moore HM, Morente M, Naimi BY, Oelmueller U, Ollier B, Parodi B, Ruan L, Stanta G, Turano P, Vaught J, Watson P, Wichmann HE, Yuille M, Zaomi M, Zatloukal K, Dagher G.

Biopreserv Biobank. 2017 Jun;15(3):270-276. doi: 10.1089/bio.2016.0053. Epub 2016 Dec 19. No abstract available.

23.

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.

Jemt A, Salmén F, Lundmark A, Mollbrink A, Fernández Navarro J, Ståhl PL, Yucel-Lindberg T, Lundeberg J.

Sci Rep. 2016 Nov 16;6:37137. doi: 10.1038/srep37137. Erratum in: Sci Rep. 2017 Mar 13;7:41109.

24.

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.

25.

Rationale and design of the PREFERS (Preserved and Reduced Ejection Fraction Epidemiological Regional Study) Stockholm heart failure study: an epidemiological regional study in Stockholm county of 2.1 million inhabitants.

Linde C, Eriksson MJ, Hage C, Wallén H, Persson B, Corbascio M, Lundeberg J, Maret E, Ugander M, Persson H; Stockholm County/Karolinska Institutet 4D heart failure investigators.

Eur J Heart Fail. 2016 Oct;18(10):1287-1297. doi: 10.1002/ejhf.599. Epub 2016 Jul 7.

26.

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.

27.

Multiplex PCB-based electrochemical detection of cancer biomarkers using MLPA-barcode approach.

Sánchez JL, Henry OY, Joda H, Solnestam BW, Kvastad L, Johansson E, Akan P, Lundeberg J, Lladach N, Ramakrishnan D, Riley I, O'Sullivan CK.

Biosens Bioelectron. 2016 Aug 15;82:224-32. doi: 10.1016/j.bios.2016.04.018. Epub 2016 Apr 7.

PMID:
27085955
28.

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.

29.

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.

30.

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.

31.

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.

32.

Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities.

Gréen H, Hasmats J, Kupershmidt I, Edsgärd D, de Petris L, Lewensohn R, Blackhall F, Vikingsson S, Besse B, Lindgren A, Brandén E, Koyi H, Peterson C, Lundeberg J.

Clin Cancer Res. 2016 Jan 15;22(2):366-73. doi: 10.1158/1078-0432.CCR-15-0964. Epub 2015 Sep 16.

33.

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.

34.

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.

35.

Nanopore arrays in a silicon membrane for parallel single-molecule detection: DNA translocation.

Zhang M, Schmidt T, Jemt A, Sahlén P, Sychugov I, Lundeberg J, Linnros J.

Nanotechnology. 2015 Aug 7;26(31):314002. doi: 10.1088/0957-4484/26/31/314002. Epub 2015 Jul 16.

PMID:
26180050
36.

Toward Rare Blood Cell Preservation for RNA Sequencing.

Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J.

J Mol Diagn. 2015 Jul;17(4):352-9. doi: 10.1016/j.jmoldx.2015.03.009. Epub 2015 May 16.

PMID:
25989392
37.

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.

38.

A validated liquid chromatography tandem mass spectrometry method for quantification of erlotinib, OSI-420 and didesmethyl erlotinib and semi-quantification of erlotinib metabolites in human plasma.

Svedberg A, Gréen H, Vikström A, Lundeberg J, Vikingsson S.

J Pharm Biomed Anal. 2015 Mar 25;107:186-95. doi: 10.1016/j.jpba.2014.12.022. Epub 2014 Dec 25.

39.

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.

40.

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.

41.

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.

42.

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.

43.

The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.

Lindholm ME, Huss M, Solnestam BW, Kjellqvist S, Lundeberg J, Sundberg CJ.

FASEB J. 2014 Oct;28(10):4571-81. doi: 10.1096/fj.14-255000. Epub 2014 Jul 11.

PMID:
25016029
44.

Fabrication and functionalization of PCB gold electrodes suitable for DNA-based electrochemical sensing.

Salvo P, Henry OY, Dhaenens K, Acero Sanchez JL, Gielen A, Werne Solnestam B, Lundeberg J, O'Sullivan CK, Vanfleteren J.

Biomed Mater Eng. 2014;24(4):1705-14. doi: 10.3233/BME-140982.

PMID:
24948454
45.

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.

46.

Forensic informativity of ~3000 bp of coding sequence of domestic dog mtDNA.

Angleby H, Oskarsson M, Pang J, Zhang YP, Leitner T, Braham C, Arvestad L, Lundeberg J, Webb KM, Savolainen P.

J Forensic Sci. 2014 Jul;59(4):898-908. doi: 10.1111/1556-4029.12504. Epub 2014 May 11.

PMID:
24814664
47.

The age and genomic integrity of neurons after cortical stroke in humans.

Huttner HB, Bergmann O, Salehpour M, Rácz A, Tatarishvili J, Lindgren E, Csonka T, Csiba L, Hortobágyi T, Méhes G, Englund E, Solnestam BW, Zdunek S, Scharenberg C, Ström L, Ståhl P, Sigurgeirsson B, Dahl A, Schwab S, Possnert G, Bernard S, Kokaia Z, Lindvall O, Lundeberg J, Frisén J.

Nat Neurosci. 2014 Jun;17(6):801-3. doi: 10.1038/nn.3706. Epub 2014 Apr 20.

PMID:
24747576
48.

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.

49.

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.

50.

Visual detection of DNA on paper chips.

Song Y, Gyarmati P, Araújo AC, Lundeberg J, Brumer H 3rd, Ståhl PL.

Anal Chem. 2014 Feb 4;86(3):1575-82. doi: 10.1021/ac403196b. Epub 2014 Jan 17.

PMID:
24383957

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