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Items: 27

1.

The complete costs of genome sequencing: a microcosting study in cancer and rare diseases from a single center in the United Kingdom.

Schwarze K, Buchanan J, Fermont JM, Dreau H, Tilley MW, Taylor JM, Antoniou P, Knight SJL, Camps C, Pentony MM, Kvikstad EM, Harris S, Popitsch N, Pagnamenta AT, Schuh A, Taylor JC, Wordsworth S.

Genet Med. 2019 Jul 30. doi: 10.1038/s41436-019-0618-7. [Epub ahead of print]

PMID:
31358947
2.

Sequencing of human genomes with nanopore technology.

Bowden R, Davies RW, Heger A, Pagnamenta AT, de Cesare M, Oikkonen LE, Parkes D, Freeman C, Dhalla F, Patel SY, Popitsch N, Ip CLC, Roberts HE, Salatino S, Lockstone H, Lunter G, Taylor JC, Buck D, Simpson MA, Donnelly P.

Nat Commun. 2019 Apr 23;10(1):1869. doi: 10.1038/s41467-019-09637-5.

3.

CD371 cell surface expression: a unique feature of DUX4-rearranged acute lymphoblastic leukemia.

Schumich A, Zaliova M, Fortschegger K, Nebral K, Attarbaschi A, Fiser K, Kauer MO, Popitsch N, Haslinger S, Inthal A, Buldini B, Basso G, Bourquin JP, Gaipa G, Brüggemann M, Feuerstein T, Maurer-Granofszky M, Panzer-Grümayer R, Trka J, Mann G, Haas OA, Hrusak O, Dworzak MN, Strehl S.

Haematologica. 2019 Aug;104(8):e352-e355. doi: 10.3324/haematol.2018.214353. Epub 2019 Jan 31. No abstract available.

4.

DeepSNP: An End-to-End Deep Neural Network with Attention-Based Localization for Breakpoint Detection in Single-Nucleotide Polymorphism Array Genomic Data.

Eghbal-Zadeh H, Fischer L, Popitsch N, Kromp F, Taschner-Mandl S, Gerber T, Bozsaky E, Ambros PF, Ambros IM, Widmer G, Moser BA.

J Comput Biol. 2019 Jun;26(6):572-596. doi: 10.1089/cmb.2018.0172. Epub 2018 Dec 26.

PMID:
30585743
5.

Shep interacts with posttranscriptional regulators to control dendrite morphogenesis in sensory neurons.

Olesnicky EC, Antonacci S, Popitsch N, Lybecker MC, Titus MB, Valadez R, Derkach PG, Marean A, Miller K, Mathai SK, Killian DJ.

Dev Biol. 2018 Dec 15;444(2):116-128. doi: 10.1016/j.ydbio.2018.09.022. Epub 2018 Oct 21.

PMID:
30352216
6.

VARAN-GIE: curation of genomic interval sets.

Popitsch N.

Bioinformatics. 2019 Mar 1;35(5):868-870. doi: 10.1093/bioinformatics/bty723.

PMID:
30137307
7.

Impaired plasticity of macrophages in X-linked adrenoleukodystrophy.

Weinhofer I, Zierfuss B, Hametner S, Wagner M, Popitsch N, Machacek C, Bartolini B, Zlabinger G, Ohradanova-Repic A, Stockinger H, Köhler W, Höftberger R, Regelsberger G, Forss-Petter S, Lassmann H, Berger J.

Brain. 2018 Aug 1;141(8):2329-2342. doi: 10.1093/brain/awy127.

8.

Clinically actionable mutation profiles in patients with cancer identified by whole-genome sequencing.

Schuh A, Dreau H, Knight SJL, Ridout K, Mizani T, Vavoulis D, Colling R, Antoniou P, Kvikstad EM, Pentony MM, Hamblin A, Protheroe A, Parton M, Shah KA, Orosz Z, Athanasou N, Hassan B, Flanagan AM, Ahmed A, Winter S, Harris A, Tomlinson I, Popitsch N, Church D, Taylor JC.

Cold Spring Harb Mol Case Stud. 2018 Apr 2;4(2). pii: a002279. doi: 10.1101/mcs.a002279. Print 2018 Apr.

9.

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.

Robbe P, Popitsch N, Knight SJL, Antoniou P, Becq J, He M, Kanapin A, Samsonova A, Vavoulis DV, Ross MT, Kingsbury Z, Cabes M, Ramos SDC, Page S, Dreau H, Ridout K, Jones LJ, Tuff-Lacey A, Henderson S, Mason J, Buffa FM, Verrill C, Maldonado-Perez D, Roxanis I, Collantes E, Browning L, Dhar S, Damato S, Davies S, Caulfield M, Bentley DR, Taylor JC, Turnbull C, Schuh A; 100,000 Genomes Project.

Genet Med. 2018 Oct;20(10):1196-1205. doi: 10.1038/gim.2017.241. Epub 2018 Feb 1.

10.

Natural RNA Polymerase Aptamers Regulate Transcription in E. coli.

Sedlyarova N, Rescheneder P, Magán A, Popitsch N, Rziha N, Bilusic I, Epshtein V, Zimmermann B, Lybecker M, Sedlyarov V, Schroeder R, Nudler E.

Mol Cell. 2017 Jul 6;67(1):30-43.e6. doi: 10.1016/j.molcel.2017.05.025. Epub 2017 Jun 22.

11.

Next-Generation Sequencing-based genomic profiling of brain metastases of primary ovarian cancer identifies high number of BRCA-mutations.

Balendran S, Liebmann-Reindl S, Berghoff AS, Reischer T, Popitsch N, Geier CB, Kenner L, Birner P, Streubel B, Preusser M.

J Neurooncol. 2017 Jul;133(3):469-476. doi: 10.1007/s11060-017-2459-z. Epub 2017 May 11.

12.

Whole-genome sequencing identifies homozygous BRCA2 deletion guiding treatment in dedifferentiated prostate cancer.

Purshouse K, Schuh A, Fairfax BP, Knight S, Antoniou P, Dreau H, Popitsch N, Gatter K, Roberts I, Browning L, Traill Z, Kerr D, Verrill C, Tuthill M, Taylor JC, Protheroe A.

Cold Spring Harb Mol Case Stud. 2017 May;3(3):a001362. doi: 10.1101/mcs.a001362.

13.

Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders.

Pagnamenta AT, Murakami Y, Taylor JM, Anzilotti C, Howard MF, Miller V, Johnson DS, Tadros S, Mansour S, Temple IK, Firth R, Rosser E, Harrison RE, Kerr B, Popitsch N; DDD Study, Kinoshita T, Taylor JC, Kini U.

Eur J Hum Genet. 2017 Jun;25(6):669-679. doi: 10.1038/ejhg.2017.32. Epub 2017 Mar 22.

14.

Temperature-dependent sRNA transcriptome of the Lyme disease spirochete.

Popitsch N, Bilusic I, Rescheneder P, Schroeder R, Lybecker M.

BMC Genomics. 2017 Jan 5;18(1):28. doi: 10.1186/s12864-016-3398-3.

15.

In vivo expression technology and 5' end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection.

Adams PP, Flores Avile C, Popitsch N, Bilusic I, Schroeder R, Lybecker M, Jewett MW.

Nucleic Acids Res. 2017 Jan 25;45(2):775-792. doi: 10.1093/nar/gkw1180. Epub 2016 Dec 1.

16.

Targeted Next-Generation Sequencing of Plasma DNA from Cancer Patients: Factors Influencing Consistency with Tumour DNA and Prospective Investigation of Its Utility for Diagnosis.

Kaisaki PJ, Cutts A, Popitsch N, Camps C, Pentony MM, Wilson G, Page S, Kaur K, Vavoulis D, Henderson S, Gupta A, Middleton MR, Karydis I, Talbot DC, Schuh A, Taylor JC.

PLoS One. 2016 Sep 14;11(9):e0162809. doi: 10.1371/journal.pone.0162809. eCollection 2016.

17.

ReliableGenome: annotation of genomic regions with high/low variant calling concordance.

Popitsch N; WGS500 Consortium, Schuh A, Taylor JC.

Bioinformatics. 2017 Jan 15;33(2):155-160. doi: 10.1093/bioinformatics/btw587. Epub 2016 Sep 7.

18.

Correction: The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation.

Drecktrah D, Lybecker M, Popitsch N, Rescheneder P, Hall LS, Samuels DS.

PLoS Pathog. 2015 Oct 16;11(10):e1005242. doi: 10.1371/journal.ppat.1005242. eCollection 2015 Oct. No abstract available.

19.

The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation.

Drecktrah D, Lybecker M, Popitsch N, Rescheneder P, Hall LS, Samuels DS.

PLoS Pathog. 2015 Sep 15;11(9):e1005160. doi: 10.1371/journal.ppat.1005160. eCollection 2015 Sep. Erratum in: PLoS Pathog. 2015 Oct;11(10):e1005242.

20.

Mutations in PIGY: expanding the phenotype of inherited glycosylphosphatidylinositol deficiencies.

Ilkovski B, Pagnamenta AT, O'Grady GL, Kinoshita T, Howard MF, Lek M, Thomas B, Turner A, Christodoulou J, Sillence D, Knight SJ, Popitsch N, Keays DA, Anzilotti C, Goriely A, Waddell LB, Brilot F, North KN, Kanzawa N, Macarthur DG, Taylor JC, Kini U, Murakami Y, Clarke NF.

Hum Mol Genet. 2015 Nov 1;24(21):6146-59. doi: 10.1093/hmg/ddv331. Epub 2015 Aug 20.

21.

Spectrum of gene mutations detected by next generation exome sequencing in brain metastases of lung adenocarcinoma.

Preusser M, Berghoff AS, Koller R, Zielinski CC, Hainfellner JA, Liebmann-Reindl S, Popitsch N, Geier CB, Streubel B, Birner P.

Eur J Cancer. 2015 Sep;51(13):1803-11. doi: 10.1016/j.ejca.2015.06.107. Epub 2015 Jul 8.

PMID:
26164066
22.

Factors influencing success of clinical genome sequencing across a broad spectrum of disorders.

Taylor JC, Martin HC, Lise S, Broxholme J, Cazier JB, Rimmer A, Kanapin A, Lunter G, Fiddy S, Allan C, Aricescu AR, Attar M, Babbs C, Becq J, Beeson D, Bento C, Bignell P, Blair E, Buckle VJ, Bull K, Cais O, Cario H, Chapel H, Copley RR, Cornall R, Craft J, Dahan K, Davenport EE, Dendrou C, Devuyst O, Fenwick AL, Flint J, Fugger L, Gilbert RD, Goriely A, Green A, Greger IH, Grocock R, Gruszczyk AV, Hastings R, Hatton E, Higgs D, Hill A, Holmes C, Howard M, Hughes L, Humburg P, Johnson D, Karpe F, Kingsbury Z, Kini U, Knight JC, Krohn J, Lamble S, Langman C, Lonie L, Luck J, McCarthy D, McGowan SJ, McMullin MF, Miller KA, Murray L, Németh AH, Nesbit MA, Nutt D, Ormondroyd E, Oturai AB, Pagnamenta A, Patel SY, Percy M, Petousi N, Piazza P, Piret SE, Polanco-Echeverry G, Popitsch N, Powrie F, Pugh C, Quek L, Robbins PA, Robson K, Russo A, Sahgal N, van Schouwenburg PA, Schuh A, Silverman E, Simmons A, Sørensen PS, Sweeney E, Taylor J, Thakker RV, Tomlinson I, Trebes A, Twigg SR, Uhlig HH, Vyas P, Vyse T, Wall SA, Watkins H, Whyte MP, Witty L, Wright B, Yau C, Buck D, Humphray S, Ratcliffe PJ, Bell JI, Wilkie AO, Bentley D, Donnelly P, McVean G.

Nat Genet. 2015 Jul;47(7):717-726. doi: 10.1038/ng.3304. Epub 2015 May 18.

23.

Germline recessive mutations in PI4KA are associated with perisylvian polymicrogyria, cerebellar hypoplasia and arthrogryposis.

Pagnamenta AT, Howard MF, Wisniewski E, Popitsch N, Knight SJ, Keays DA, Quaghebeur G, Cox H, Cox P, Balla T, Taylor JC, Kini U.

Hum Mol Genet. 2015 Jul 1;24(13):3732-41. doi: 10.1093/hmg/ddv117. Epub 2015 Apr 8.

24.

Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation.

Bilusic I, Popitsch N, Rescheneder P, Schroeder R, Lybecker M.

RNA Biol. 2014;11(5):641-54. Epub 2014 Jun 12.

25.

CODOC: efficient access, analysis and compression of depth of coverage signals.

Popitsch N.

Bioinformatics. 2014 Sep 15;30(18):2676-7. doi: 10.1093/bioinformatics/btu362. Epub 2014 May 28.

PMID:
24872424
26.

Novel clinically relevant genes in gastrointestinal stromal tumors identified by exome sequencing.

Schoppmann SF, Vinatzer U, Popitsch N, Mittlböck M, Liebmann-Reindl S, Jomrich G, Streubel B, Birner P.

Clin Cancer Res. 2013 Oct 1;19(19):5329-39. doi: 10.1158/1078-0432.CCR-12-3863. Epub 2013 Aug 13.

27.

NGC: lossless and lossy compression of aligned high-throughput sequencing data.

Popitsch N, von Haeseler A.

Nucleic Acids Res. 2013 Jan 7;41(1):e27. doi: 10.1093/nar/gks939. Epub 2012 Oct 12.

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