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Items: 1 to 20 of 98

1.

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.

Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J.

Cell. 2019 Sep 5;178(6):1465-1477.e17. doi: 10.1016/j.cell.2019.08.018.

PMID:
31491388
2.

Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1.

Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W, Thornton JM.

Genome Biol. 2019 Aug 14;20(1):146. doi: 10.1186/s13059-019-1753-9.

3.

Induction of Neural Crest Stem Cells From Bardet-Biedl Syndrome Patient Derived hiPSCs.

Barrell WB, Griffin JN, Harvey JL; HipSci Consortium, Danovi D, Beales P, Grigoriadis AE, Liu KJ.

Front Mol Neurosci. 2019 Jun 21;12:139. doi: 10.3389/fnmol.2019.00139. eCollection 2019.

4.

Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels.

Sousa A, Gonçalves E, Mirauta B, Ochoa D, Stegle O, Beltrao P.

Mol Cell Proteomics. 2019 Aug 9;18(8 suppl 1):S114-S125. doi: 10.1074/mcp.RA118.001280. Epub 2019 Jun 25.

5.

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.

Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, Banerjee A, Kim DS, Beier T, Urban L, Kundaje A, Stegle O, Gagneur J.

Nat Biotechnol. 2019 Jun;37(6):592-600. doi: 10.1038/s41587-019-0140-0. No abstract available.

PMID:
31138913
6.

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.

Vigilante A, Laddach A, Moens N, Meleckyte R, Leha A, Ghahramani A, Culley OJ, Kathuria A, Hurling C, Vickers A, Wiseman E, Tewary M, Zandstra PW; HipSci Consortium, Durbin R, Fraternali F, Stegle O, Birney E, Luscombe NM, Danovi D, Watt FM.

Cell Rep. 2019 Feb 19;26(8):2078-2087.e3. doi: 10.1016/j.celrep.2019.01.094.

7.

Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity.

Linker SM, Urban L, Clark SJ, Chhatriwala M, Amatya S, McCarthy DJ, Ebersberger I, Vallier L, Reik W, Stegle O, Bonder MJ.

Genome Biol. 2019 Feb 11;20(1):30. doi: 10.1186/s13059-019-1644-0.

8.

Structural rearrangements generate cell-specific, gene-independent CRISPR-Cas9 loss of fitness effects.

Gonçalves E, Behan FM, Louzada S, Arnol D, Stronach EA, Yang F, Yusa K, Stegle O, Iorio F, Garnett MJ.

Genome Biol. 2019 Feb 5;20(1):27. doi: 10.1186/s13059-019-1637-z.

9.

A linear mixed-model approach to study multivariate gene-environment interactions.

Moore R, Casale FP, Jan Bonder M, Horta D; BIOS Consortium, Franke L, Barroso I, Stegle O.

Nat Genet. 2019 Jan;51(1):180-186. doi: 10.1038/s41588-018-0271-0. Epub 2018 Nov 26.

10.

The germline genetic component of drug sensitivity in cancer cell lines.

Menden MP, Casale FP, Stephan J, Bignell GR, Iorio F, McDermott U, Garnett MJ, Saez-Rodriguez J, Stegle O.

Nat Commun. 2018 Aug 23;9(1):3385. doi: 10.1038/s41467-018-05811-3.

11.

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C; Cancer Genome Atlas Research Network, Rätsch G.

Cancer Cell. 2018 Aug 13;34(2):211-224.e6. doi: 10.1016/j.ccell.2018.07.001. Epub 2018 Aug 2.

12.

Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency.

Rulands S, Lee HJ, Clark SJ, Angermueller C, Smallwood SA, Krueger F, Mohammed H, Dean W, Nichols J, Rugg-Gunn P, Kelsey G, Stegle O, Simons BD, Reik W.

Cell Syst. 2018 Jul 25;7(1):63-76.e12. doi: 10.1016/j.cels.2018.06.012.

13.

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

Argelaguet R, Velten B, Arnol D, Dietrich S, Zenz T, Marioni JC, Buettner F, Huber W, Stegle O.

Mol Syst Biol. 2018 Jun 20;14(6):e8124. doi: 10.15252/msb.20178124.

14.

Reply.

Howell K, Kraiczy J, Stegle O, Zilbauer M.

Gastroenterology. 2018 Jul;155(1):230-231. doi: 10.1053/j.gastro.2018.06.033. Epub 2018 Jun 9. No abstract available.

PMID:
29894680
15.

Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Casale FP, Wolford BN, Guan L, Varshney A, Albanus RD, Parker SCJ, Narisu N, Chines PS, Erdos MR, Welch RP, Kinnunen L, Saramies J, Sundvall J, Lakka TA, Laakso M, Tuomilehto J, Koistinen HA, Stegle O, Boehnke M, Birney E, Collins FS.

PLoS One. 2018 Apr 16;13(4):e0195788. doi: 10.1371/journal.pone.0195788. eCollection 2018.

16.

SpatialDE: identification of spatially variable genes.

Svensson V, Teichmann SA, Stegle O.

Nat Methods. 2018 May;15(5):343-346. doi: 10.1038/nmeth.4636. Epub 2018 Mar 19.

17.

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells.

Clark SJ, Argelaguet R, Kapourani CA, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W.

Nat Commun. 2018 Feb 22;9(1):781. doi: 10.1038/s41467-018-03149-4.

18.

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.

19.

Expression Atlas: gene and protein expression across multiple studies and organisms.

Papatheodorou I, Fonseca NA, Keays M, Tang YA, Barrera E, Bazant W, Burke M, Füllgrabe A, Fuentes AM, George N, Huerta L, Koskinen S, Mohammed S, Geniza M, Preece J, Jaiswal P, Jarnuczak AF, Huber W, Stegle O, Vizcaino JA, Brazma A, Petryszak R.

Nucleic Acids Res. 2018 Jan 4;46(D1):D246-D251. doi: 10.1093/nar/gkx1158.

20.

Genome-wide mapping of genetic determinants influencing DNA methylation and gene expression in human hippocampus.

Schulz H, Ruppert AK, Herms S, Wolf C, Mirza-Schreiber N, Stegle O, Czamara D, Forstner AJ, Sivalingam S, Schoch S, Moebus S, Pütz B, Hillmer A, Fricker N, Vatter H, Müller-Myhsok B, Nöthen MM, Becker AJ, Hoffmann P, Sander T, Cichon S.

Nat Commun. 2017 Nov 15;8(1):1511. doi: 10.1038/s41467-017-01818-4.

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