Pesquisa | Biblioteca Virtual em Saúde

1.

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

Demircioglu, Deniz; Cukuroglu, Engin; Kindermans, Martin; Nandi, Tannistha; Calabrese, Claudia; Fonseca, Nuno A; Kahles, André; Lehmann, Kjong-Van; Stegle, Oliver; Brazma, Alvis; Brooks, Angela N; Rätsch, Gunnar; Tan, Patrick; Göke, Jonathan.

Cell; 178(6): 1465-1477.e17, 2019 Sep 05.

Artigo em Inglês | MEDLINE | ID: mdl-31491388

2.

Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.

Cabezas-Wallscheid, Nina; Buettner, Florian; Sommerkamp, Pia; Klimmeck, Daniel; Ladel, Luisa; Thalheimer, Frederic B; Pastor-Flores, Daniel; Roma, Leticia P; Renders, Simon; Zeisberger, Petra; Przybylla, Adriana; Schönberger, Katharina; Scognamiglio, Roberta; Altamura, Sandro; Florian, Carolina M; Fawaz, Malak; Vonficht, Dominik; Tesio, Melania; Collier, Paul; Pavlinic, Dinko; Geiger, Hartmut; Schroeder, Timm; Benes, Vladimir; Dick, Tobias P; Rieger, Michael A; Stegle, Oliver; Trumpp, Andreas.

Cell; 169(5): 807-823.e19, 2017 May 18.

Artigo em Inglês | MEDLINE | ID: mdl-28479188

3.

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.

Javierre, Biola M; Burren, Oliver S; Wilder, Steven P; Kreuzhuber, Roman; Hill, Steven M; Sewitz, Sven; Cairns, Jonathan; Wingett, Steven W; Várnai, Csilla; Thiecke, Michiel J; Burden, Frances; Farrow, Samantha; Cutler, Antony J; Rehnström, Karola; Downes, Kate; Grassi, Luigi; Kostadima, Myrto; Freire-Pritchett, Paula; Wang, Fan; Stunnenberg, Hendrik G; Todd, John A; Zerbino, Daniel R; Stegle, Oliver; Ouwehand, Willem H; Frontini, Mattia; Wallace, Chris; Spivakov, Mikhail; Fraser, Peter.

Cell; 167(5): 1369-1384.e19, 2016 11 17.

Artigo em Inglês | MEDLINE | ID: mdl-27863249

4.

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.

Angermueller, Christof; Clark, Stephen J; Lee, Heather J; Macaulay, Iain C; Teng, Mabel J; Hu, Tim Xiaoming; Krueger, Felix; Smallwood, Sebastien; Ponting, Chris P; Voet, Thierry; Kelsey, Gavin; Stegle, Oliver; Reik, Wolf.

Nat Methods; 13(3): 229-232, 2016 Mar.

Artigo em Inglês | MEDLINE | ID: mdl-26752769

5.

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.

Smallwood, Sébastien A; Lee, Heather J; Angermueller, Christof; Krueger, Felix; Saadeh, Heba; Peat, Julian; Andrews, Simon R; Stegle, Oliver; Reik, Wolf; Kelsey, Gavin.

Nat Methods; 11(8): 817-820, 2014 Aug.

Artigo em Inglês | MEDLINE | ID: mdl-25042786

6.

Genetic variants regulating expression levels and isoform diversity during embryogenesis.

Cannavò, Enrico; Koelling, Nils; Harnett, Dermot; Garfield, David; Casale, Francesco P; Ciglar, Lucia; Gustafson, Hilary E; Viales, Rebecca R; Marco-Ferreres, Raquel; Degner, Jacob F; Zhao, Bingqing; Stegle, Oliver; Birney, Ewan; Furlong, Eileen E M.

Nature; 541(7637): 402-406, 2017 01 19.

Artigo em Inglês | MEDLINE | ID: mdl-28024300

7.

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.

Kilpinen, Helena; Goncalves, Angela; Leha, Andreas; Afzal, Vackar; Alasoo, Kaur; Ashford, Sofie; Bala, Sendu; Bensaddek, Dalila; Casale, Francesco Paolo; Culley, Oliver J; Danecek, Petr; Faulconbridge, Adam; Harrison, Peter W; Kathuria, Annie; McCarthy, Davis; McCarthy, Shane A; Meleckyte, Ruta; Memari, Yasin; Moens, Nathalie; Soares, Filipa; Mann, Alice; Streeter, Ian; Agu, Chukwuma A; Alderton, Alex; Nelson, Rachel; Harper, Sarah; Patel, Minal; White, Alistair; Patel, Sharad R; Clarke, Laura; Halai, Reena; Kirton, Christopher M; Kolb-Kokocinski, Anja; Beales, Philip; Birney, Ewan; Danovi, Davide; Lamond, Angus I; Ouwehand, Willem H; Vallier, Ludovic; Watt, Fiona M; Durbin, Richard; Stegle, Oliver; Gaffney, Daniel J.

Nature; 546(7660): 686, 2017 06 29.

Artigo em Inglês | MEDLINE | ID: mdl-28614302

8.

Common genetic variation drives molecular heterogeneity in human iPSCs.

Kilpinen, Helena; Goncalves, Angela; Leha, Andreas; Afzal, Vackar; Alasoo, Kaur; Ashford, Sofie; Bala, Sendu; Bensaddek, Dalila; Casale, Francesco Paolo; Culley, Oliver J; Danecek, Petr; Faulconbridge, Adam; Harrison, Peter W; Kathuria, Annie; McCarthy, Davis; McCarthy, Shane A; Meleckyte, Ruta; Memari, Yasin; Moens, Nathalie; Soares, Filipa; Mann, Alice; Streeter, Ian; Agu, Chukwuma A; Alderton, Alex; Nelson, Rachel; Harper, Sarah; Patel, Minal; White, Alistair; Patel, Sharad R; Clarke, Laura; Halai, Reena; Kirton, Christopher M; Kolb-Kokocinski, Anja; Beales, Philip; Birney, Ewan; Danovi, Davide; Lamond, Angus I; Ouwehand, Willem H; Vallier, Ludovic; Watt, Fiona M; Durbin, Richard; Stegle, Oliver; Gaffney, Daniel J.

Nature; 546(7658): 370-375, 2017 06 15.

Artigo em Inglês | MEDLINE | ID: mdl-28489815

9.

SpatialDE: identification of spatially variable genes.

Svensson, Valentine; Teichmann, Sarah A; Stegle, Oliver.

Nat Methods; 15(5): 343-346, 2018 May.

Artigo em Inglês | MEDLINE | ID: mdl-29553579

10.

Computational and analytical challenges in single-cell transcriptomics.

Stegle, Oliver; Teichmann, Sarah A; Marioni, John C.

Nat Rev Genet; 16(3): 133-45, 2015 Mar.

Artigo em Inglês | MEDLINE | ID: mdl-25628217

11.

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

Sousa, Abel; Gonçalves, Emanuel; Mirauta, Bogdan; Ochoa, David; Stegle, Oliver; Beltrao, Pedro.

Mol Cell Proteomics; 18(8 suppl 1): S114-S125, 2019 Aug 09.

Artigo em Inglês | MEDLINE | ID: mdl-31239291

12.

easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.

Grimm, Dominik G; Roqueiro, Damian; Salomé, Patrice A; Kleeberger, Stefan; Greshake, Bastian; Zhu, Wangsheng; Liu, Chang; Lippert, Christoph; Stegle, Oliver; Schölkopf, Bernhard; Weigel, Detlef; Borgwardt, Karsten M.

Plant Cell; 29(1): 5-19, 2017 01.

Artigo em Inglês | MEDLINE | ID: mdl-27986896

13.

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

Papatheodorou, Irene; Fonseca, Nuno A; Keays, Maria; Tang, Y Amy; Barrera, Elisabet; Bazant, Wojciech; Burke, Melissa; Füllgrabe, Anja; Fuentes, Alfonso Muñoz-Pomer; George, Nancy; Huerta, Laura; Koskinen, Satu; Mohammed, Suhaib; Geniza, Matthew; Preece, Justin; Jaiswal, Pankaj; Jarnuczak, Andrew F; Huber, Wolfgang; Stegle, Oliver; Vizcaino, Juan Antonio; Brazma, Alvis; Petryszak, Robert.

Nucleic Acids Res; 46(D1): D246-D251, 2018 Jan 04.

Artigo em Inglês | MEDLINE | ID: mdl-29165655

14.

Joint genetic analysis using variant sets reveals polygenic gene-context interactions.

Casale, Francesco Paolo; Horta, Danilo; Rakitsch, Barbara; Stegle, Oliver.

PLoS Genet; 13(4): e1006693, 2017 04.

Artigo em Inglês | MEDLINE | ID: mdl-28426829

15.

Genetic Variation in the Social Environment Contributes to Health and Disease.

Baud, Amelie; Mulligan, Megan K; Casale, Francesco Paolo; Ingels, Jesse F; Bohl, Casey J; Callebert, Jacques; Launay, Jean-Marie; Krohn, Jon; Legarra, Andres; Williams, Robert W; Stegle, Oliver.

PLoS Genet; 13(1): e1006498, 2017 01.

Artigo em Inglês | MEDLINE | ID: mdl-28121987

16.

DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.

Howell, Kate Joanne; Kraiczy, Judith; Nayak, Komal M; Gasparetto, Marco; Ross, Alexander; Lee, Claire; Mak, Tim N; Koo, Bon-Kyoung; Kumar, Nitin; Lawley, Trevor; Sinha, Anupam; Rosenstiel, Philip; Heuschkel, Robert; Stegle, Oliver; Zilbauer, Matthias.

Gastroenterology; 154(3): 585-598, 2018 02.

Artigo em Inglês | MEDLINE | ID: mdl-29031501

17.

Phosphonormalizer: an R package for normalization of MS-based label-free phosphoproteomics.

Saraei, Sohrab; Suomi, Tomi; Kauko, Otto; Elo, Laura L; Stegle, Oliver.

Bioinformatics; 34(4): 693-694, 2018 02 15.

Artigo em Inglês | MEDLINE | ID: mdl-28968644

18.

Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data.

Serra, Angela; Coretto, Pietro; Fratello, Michele; Tagliaferri, Roberto; Stegle, Oliver.

Bioinformatics; 34(4): 625-634, 2018 02 15.

Artigo em Inglês | MEDLINE | ID: mdl-29040390

19.

An omnibus test for differential distribution analysis of microbiome sequencing data.

Chen, Jun; King, Emily; Deek, Rebecca; Wei, Zhi; Yu, Yue; Grill, Diane; Ballman, Karla; Stegle, Oliver.

Bioinformatics; 34(4): 643-651, 2018 02 15.

Artigo em Inglês | MEDLINE | ID: mdl-29040451

20.

Applying family analyses to electronic health records to facilitate genetic research.

Huang, Xiayuan; Elston, Robert C; Rosa, Guilherme J; Mayer, John; Ye, Zhan; Kitchner, Terrie; Brilliant, Murray H; Page, David; Hebbring, Scott J; Stegle, Oliver.

Bioinformatics; 34(4): 635-642, 2018 02 15.

Artigo em Inglês | MEDLINE | ID: mdl-28968884

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