Publications by authors named "Oliver Stegle"

100Publications

The Polygenic and Monogenic Basis of Blood Traits and Diseases.

Authors:
Dragana Vuckovic Erik L Bao Parsa Akbari Caleb A Lareau Abdou Mousas Tao Jiang Ming-Huei Chen Laura M Raffield Manuel Tardaguila Jennifer E Huffman Scott C Ritchie Karyn Megy Hannes Ponstingl Christopher J Penkett Patrick K Albers Emilie M Wigdor Saori Sakaue Arden Moscati Regina Manansala Ken Sin Lo Huijun Qian Masato Akiyama Traci M Bartz Yoav Ben-Shlomo Andrew Beswick Jette Bork-Jensen Erwin P Bottinger Jennifer A Brody Frank J A van Rooij Kumaraswamy N Chitrala Peter W F Wilson Hélène Choquet John Danesh Emanuele Di Angelantonio Niki Dimou Jingzhong Ding Paul Elliott Tõnu Esko Michele K Evans Stephan B Felix James S Floyd Linda Broer Niels Grarup Michael H Guo Qi Guo Andreas Greinacher Jeff Haessler Torben Hansen Joanna M M Howson Wei Huang Eric Jorgenson Tim Kacprowski Mika Kähönen Yoichiro Kamatani Masahiro Kanai Savita Karthikeyan Fotios Koskeridis Leslie A Lange Terho Lehtimäki Allan Linneberg Yongmei Liu Leo-Pekka Lyytikäinen Ani Manichaikul Koichi Matsuda Karen L Mohlke Nina Mononen Yoshinori Murakami Girish N Nadkarni Kjell Nikus Nathan Pankratz Oluf Pedersen Michael Preuss Bruce M Psaty Olli T Raitakari Stephen S Rich Benjamin A T Rodriguez Jonathan D Rosen Jerome I Rotter Petra Schubert Cassandra N Spracklen Praveen Surendran Hua Tang Jean-Claude Tardif Mohsen Ghanbari Uwe Völker Henry Völzke Nicholas A Watkins Stefan Weiss Na Cai Kousik Kundu Stephen B Watt Klaudia Walter Alan B Zonderman Kelly Cho Yun Li Ruth J F Loos Julian C Knight Michel Georges Oliver Stegle Evangelos Evangelou Yukinori Okada David J Roberts Michael Inouye Andrew D Johnson Paul L Auer William J Astle Alexander P Reiner Adam S Butterworth Willem H Ouwehand Guillaume Lettre Vijay G Sankaran Nicole Soranzo

Cell 2020 Sep;182(5):1214-1231.e11

Human Genetics, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK; National Institute for Health Research Blood and Transplant Research Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, CB1 8RN, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK; Department of Haematology, University of Cambridge, Cambridge, CB2 0PT, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2020.08.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7482360PMC
September 2020

Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation.

Cell Stem Cell 2020 Sep 13;27(3):470-481.e6. Epub 2020 Aug 13.

Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2020.07.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487768PMC
September 2020

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program.

Cell Syst 2020 Jul 6;11(1):25-41.e9. Epub 2020 Jul 6.

Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Centre for Trophoblast Research University of Cambridge, Cambridge CB2 3EG, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2020.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7383230PMC
July 2020

MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data.

Genome Biol 2020 05 11;21(1):111. Epub 2020 May 11.

European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-020-02015-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212577PMC
May 2020

Effects of the COVID-19 pandemic on life scientists.

Genome Biol 2020 05 11;21(1):113. Epub 2020 May 11.

European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-020-02031-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7212246PMC
May 2020

Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.

Nat Methods 2020 04 16;17(4):414-421. Epub 2020 Mar 16.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41592-020-0766-3DOI Listing
April 2020

Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.

Genome Biol 2020 02 12;21(1):36. Epub 2020 Feb 12.

Institute for Computational Biomedicine, Bioquant, Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Heidelberg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-020-1949-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017576PMC
February 2020

Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.

Genome Biol 2019 12 13;20(1):273. Epub 2019 Dec 13.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-019-1865-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6909514PMC
December 2019

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.

Cell Rep 2019 10;29(1):202-211.e6

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany; Division of Computational Genomics and Systems Genetics, German Cancer Research Center, 69120 Heidelberg, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2019.08.077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6899515PMC
October 2019

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

Cell 2019 09;178(6):1465-1477.e17

Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore 169610, Singapore. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2019.08.018DOI Listing
September 2019

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

Mol Cell Proteomics 2019 08 25;18(8 suppl 1):S114-S125. Epub 2019 Jun 25.

‖European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, Cambridge, UK

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1074/mcp.RA118.001280DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692786PMC
August 2019

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

Nat Genet 2019 01 26;51(1):180-186. Epub 2018 Nov 26.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41588-018-0271-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354905PMC
January 2019

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

Nat Commun 2018 08 23;9(1):3385. Epub 2018 Aug 23.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/s41467-018-05811-3
Publisher Site
http://dx.doi.org/10.1038/s41467-018-05811-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6107640PMC
August 2018

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

Cancer Cell 2018 08 2;34(2):211-224.e6. Epub 2018 Aug 2.

ETH Zurich, Department of Computer Science, Zurich, Switzerland; Memorial Sloan Kettering Cancer Center, Computational Biology Department, New York, USA; University Hospital Zurich, Biomedical Informatics Research, Zurich, Switzerland; ETH Zurich, Department of Biology, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ccell.2018.07.001DOI Listing
August 2018

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

Cell Syst 2018 07;7(1):63-76.e12

Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK; Epigenetics Programme, Babraham Institute, Cambridge, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2018.06.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6066359PMC
July 2018

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

Mol Syst Biol 2018 06 20;14(6):e8124. Epub 2018 Jun 20.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, UK

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6010767PMC
http://dx.doi.org/10.15252/msb.20178124DOI Listing
June 2018

Reply.

Gastroenterology 2018 07 9;155(1):230-231. Epub 2018 Jun 9.

University Department of Paediatrics, University of Cambridge, Cambridge, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1053/j.gastro.2018.06.033DOI Listing
July 2018

SpatialDE: identification of spatially variable genes.

Nat Methods 2018 05 19;15(5):343-346. Epub 2018 Mar 19.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.4636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350895PMC
May 2018

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

Genome Biol 2017 11 7;18(1):212. Epub 2017 Nov 7.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

View Article

Download full-text PDF

Source
https://genomebiology.biomedcentral.com/articles/10.1186/s13
Publisher Site
http://dx.doi.org/10.1186/s13059-017-1334-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5674756PMC
November 2017

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

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

Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, NY 10065, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx650DOI Listing
February 2018

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

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

NeuRoNeLab, Department of Management and Innovation Systems, University of Salerno, Fisciano (Sa), 84084, Italy.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx642DOI Listing
February 2018

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

Gastroenterology 2018 02 12;154(3):585-598. Epub 2017 Oct 12.

University Department of Paediatrics, University of Cambridge, UK; Department of Paediatric Gastroenterology, University of Cambridge and Addenbrooke's Hospital, Cambridge, UK; Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1053/j.gastro.2017.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6381389PMC
February 2018

Single-cell epigenomics: Recording the past and predicting the future.

Science 2017 10;358(6359):69-75

Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1126/science.aan6826DOI Listing
October 2017

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

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

Bioinformatics Unit, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Tykistökatu 6, FI-20520 Turku, Finland.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btx573DOI Listing
February 2018

Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.

Authors:
Ioanna Tachmazidou Dániel Süveges Josine L Min Graham R S Ritchie Julia Steinberg Klaudia Walter Valentina Iotchkova Jeremy Schwartzentruber Jie Huang Yasin Memari Shane McCarthy Andrew A Crawford Cristina Bombieri Massimiliano Cocca Aliki-Eleni Farmaki Tom R Gaunt Pekka Jousilahti Marjolein N Kooijman Benjamin Lehne Giovanni Malerba Satu Männistö Angela Matchan Carolina Medina-Gomez Sarah J Metrustry Abhishek Nag Ioanna Ntalla Lavinia Paternoster Nigel W Rayner Cinzia Sala William R Scott Hashem A Shihab Lorraine Southam Beate St Pourcain Michela Traglia Katerina Trajanoska Gialuigi Zaza Weihua Zhang María S Artigas Narinder Bansal Marianne Benn Zhongsheng Chen Petr Danecek Wei-Yu Lin Adam Locke Jian'an Luan Alisa K Manning Antonella Mulas Carlo Sidore Anne Tybjaerg-Hansen Anette Varbo Magdalena Zoledziewska Chris Finan Konstantinos Hatzikotoulas Audrey E Hendricks John P Kemp Alireza Moayyeri Kalliope Panoutsopoulou Michal Szpak Scott G Wilson Michael Boehnke Francesco Cucca Emanuele Di Angelantonio Claudia Langenberg Cecilia Lindgren Mark I McCarthy Andrew P Morris Børge G Nordestgaard Robert A Scott Martin D Tobin Nicholas J Wareham Paul Burton John C Chambers George Davey Smith George Dedoussis Janine F Felix Oscar H Franco Giovanni Gambaro Paolo Gasparini Christopher J Hammond Albert Hofman Vincent W V Jaddoe Marcus Kleber Jaspal S Kooner Markus Perola Caroline Relton Susan M Ring Fernando Rivadeneira Veikko Salomaa Timothy D Spector Oliver Stegle Daniela Toniolo André G Uitterlinden Inês Barroso Celia M T Greenwood John R B Perry Brian R Walker Adam S Butterworth Yali Xue Richard Durbin Kerrin S Small Nicole Soranzo Nicholas J Timpson Eleftheria Zeggini

Am J Hum Genet 2017 Jun 25;100(6):865-884. Epub 2017 May 25.

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ajhg.2017.04.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5473732PMC
June 2017

Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.

Genome Biol 2017 05 12;18(1):90. Epub 2017 May 12.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-017-1233-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5429579PMC
May 2017

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

Cell 2017 May 4;169(5):807-823.e19. Epub 2017 May 4.

Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cell.2017.04.018DOI Listing
May 2017

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

PLoS Genet 2017 04 20;13(4):e1006693. Epub 2017 Apr 20.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, CB10 1SD Hinxton, Cambridge, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1006693DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5398484PMC
April 2017

Multi-tissue DNA methylation age predictor in mouse.

Genome Biol 2017 04 11;18(1):68. Epub 2017 Apr 11.

Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-017-1203-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389178PMC
April 2017

DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.

Genome Biol 2017 Apr 11;18(1):67. Epub 2017 Apr 11.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-017-1189-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5387360PMC
April 2017

Promoter shape varies across populations and affects promoter evolution and expression noise.

Nat Genet 2017 Apr 13;49(4):550-558. Epub 2017 Feb 13.

European Molecular Biology Laboratory (EMBL) Genome Biology Unit, Heidelberg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.3791DOI Listing
April 2017

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

PLoS Genet 2017 01 25;13(1):e1006498. Epub 2017 Jan 25.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1006498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5266220PMC
January 2017

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

Plant Cell 2017 01 16;29(1):5-19. Epub 2016 Dec 16.

Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1105/tpc.16.00551DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5304348PMC
January 2017

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.

Cell 2016 11;167(5):1398-1414.e24

Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00928674163144
Publisher Site
http://dx.doi.org/10.1016/j.cell.2016.10.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5119954PMC
November 2016

Deep learning for computational biology.

Mol Syst Biol 2016 07 29;12(7):878. Epub 2016 Jul 29.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton Cambridge, UK

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4965871PMC
http://dx.doi.org/10.15252/msb.20156651DOI Listing
July 2016

Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.

PLoS Genet 2016 07 11;12(7):e1006141. Epub 2016 Jul 11.

Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1006141DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939946PMC
July 2016

GeneCodeq: quality score compression and improved genotyping using a Bayesian framework.

Bioinformatics 2016 10 26;32(20):3124-3132. Epub 2016 Jun 26.

PetaGene, Ideaspace, 3 Charles Babbage Rd, Cambridge CB3 0GT, UK.

View Article

Download full-text PDF

Source
http://bioinformatics.oxfordjournals.org/content/early/2016/
Web Search
http://dx.doi.org/10.1093/bioinformatics/btw385DOI Listing
October 2016

Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.

Genome Biol 2016 Feb 24;17:33. Epub 2016 Feb 24.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-016-0895-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765046PMC
February 2016

A high-content platform to characterise human induced pluripotent stem cell lines.

Methods 2016 Mar 25;96:85-96. Epub 2015 Nov 25.

HipSci Cell Phenotyping, Centre for Stem Cells and Regenerative Medicine, King's College London, Great Maze Pond, London SE1 9RT, UK. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2015.11.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4773406PMC
March 2016

An integrated map of structural variation in 2,504 human genomes.

Nature 2015 Oct;526(7571):75-81

European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstr. 1, 69117 Heidelberg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature15394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617611PMC
October 2015

Computational assignment of cell-cycle stage from single-cell transcriptome data.

Methods 2015 Sep 2;85:54-61. Epub 2015 Jul 2.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany. Electronic address:

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S10462023153000
Publisher Site
http://dx.doi.org/10.1016/j.ymeth.2015.06.021DOI Listing
September 2015

A random forest approach to capture genetic effects in the presence of population structure.

Nat Commun 2015 Jun 25;6:7432. Epub 2015 Jun 25.

Cellular Networks and Systems Biology, University of Cologne, CECAD, Joseph-Stelzmann-Strasse 26, Cologne 50931, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms8432DOI Listing
June 2015

Efficient set tests for the genetic analysis of correlated traits.

Nat Methods 2015 Aug 15;12(8):755-8. Epub 2015 Jun 15.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.3439DOI Listing
August 2015

Genome-wide studies of verbal declarative memory in nondemented older people: the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.

Authors:
Stéphanie Debette Carla A Ibrahim Verbaas Jan Bressler Maaike Schuur Albert Smith Joshua C Bis Gail Davies Christiane Wolf Vilmundur Gudnason Lori B Chibnik Qiong Yang Anita L deStefano Dominique J F de Quervain Velandai Srikanth Jari Lahti Hans J Grabe Jennifer A Smith Lutz Priebe Lei Yu Nazanin Karbalai Caroline Hayward James F Wilson Harry Campbell Katja Petrovic Myriam Fornage Ganesh Chauhan Robin Yeo Ruth Boxall James Becker Oliver Stegle Karen A Mather Vincent Chouraki Qi Sun Lynda M Rose Susan Resnick Christopher Oldmeadow Mirna Kirin Alan F Wright Maria K Jonsdottir Rhoda Au Albert Becker Najaf Amin Mike A Nalls Stephen T Turner Sharon L R Kardia Ben Oostra Gwen Windham Laura H Coker Wei Zhao David S Knopman Gerardo Heiss Michael E Griswold Rebecca F Gottesman Veronique Vitart Nicholas D Hastie Lina Zgaga Igor Rudan Ozren Polasek Elizabeth G Holliday Peter Schofield Seung Hoan Choi Toshiko Tanaka Yang An Rodney T Perry Richard E Kennedy Michèle M Sale Jing Wang Virginia G Wadley David C Liewald Paul M Ridker Alan J Gow Alison Pattie John M Starr David Porteous Xuan Liu Russell Thomson Nicola J Armstrong Gudny Eiriksdottir Arezoo A Assareh Nicole A Kochan Elisabeth Widen Aarno Palotie Yi-Chen Hsieh Johan G Eriksson Christian Vogler John C van Swieten Joshua M Shulman Alexa Beiser Jerome Rotter Carsten O Schmidt Wolfgang Hoffmann Markus M Nöthen Luigi Ferrucci John Attia Andre G Uitterlinden Philippe Amouyel Jean-François Dartigues Hélène Amieva Katri Räikkönen Melissa Garcia Philip A Wolf Albert Hofman W T Longstreth Bruce M Psaty Eric Boerwinkle Philip L DeJager Perminder S Sachdev Reinhold Schmidt Monique M B Breteler Alexander Teumer Oscar L Lopez Sven Cichon Daniel I Chasman Francine Grodstein Bertram Müller-Myhsok Christophe Tzourio Andreas Papassotiropoulos David A Bennett M Arfan Ikram Ian J Deary Cornelia M van Duijn Lenore Launer Annette L Fitzpatrick Sudha Seshadri Thomas H Mosley

Biol Psychiatry 2015 Apr 25;77(8):749-63. Epub 2014 Nov 25.

Department of Medicine and Neurology, University of Mississippi Medical Center, Jackson, Mississippi.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.biopsych.2014.08.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4513651PMC
April 2015

Computational and analytical challenges in single-cell transcriptomics.

Nat Rev Genet 2015 Mar 28;16(3):133-45. Epub 2015 Jan 28.

1] European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. [2] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

View Article

Download full-text PDF

Source
http://sv.epfl.ch/files/content/sites/svnew2/files/shared/LS
Web Search
http://www.nature.com/doifinder/10.1038/nrg3833
Publisher Site
http://dx.doi.org/10.1038/nrg3833DOI Listing
March 2015

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

Nat Biotechnol 2015 Feb 19;33(2):155-60. Epub 2015 Jan 19.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.3102DOI Listing
February 2015

Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.

Pac Symp Biocomput 2015 :342-6

Icahn School of Medicine at Mount Sinai, 1425 Madison Ave., New York, USA.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5893135PMC
April 2016

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

Pac Symp Biocomput 2015 :44-55

Computational Biology Center, Memorial Kettering Cancer Center, New York, NY 10044, U.S.A.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333684PMC
April 2016

Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.

Plant Cell 2014 Nov 26;26(11):4298-310. Epub 2014 Nov 26.

INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France AgroParisTech, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, F-78026 Versailles, France

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1105/tpc.114.130310DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4277215PMC
November 2014

Warped linear mixed models for the genetic analysis of transformed phenotypes.

Nat Commun 2014 Sep 19;5:4890. Epub 2014 Sep 19.

European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ncomms5890DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4199105PMC
September 2014

Accurate detection of differential RNA processing.

Nucleic Acids Res 2013 May 12;41(10):5189-98. Epub 2013 Apr 12.

Computational Biology Center, Sloan-Kettering Institute, 1275 York Avenue, New York, NY 10065, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gkt211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664801PMC
May 2013

Detecting regulatory gene-environment interactions with unmeasured environmental factors.

Bioinformatics 2013 Jun 4;29(11):1382-9. Epub 2013 Apr 4.

Department of Computer Science, University of Sheffield, Sheffield, UK.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt148DOI Listing
June 2013

The future of genome-based medicine.

Pac Symp Biocomput 2013 :456-8

University of Toronto, Donnelly Centre, 160 College Street, Toronto, ON M5S 3E1, Canada.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894348PMC
December 2013

PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY.

Pac Symp Biocomput 2013 ;18:171-174

Max Planck Institutes Tübingen, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5894351PMC
January 2013

A Lasso multi-marker mixed model for association mapping with population structure correction.

Bioinformatics 2013 Jan 22;29(2):206-14. Epub 2012 Nov 22.

Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.

View Article

Download full-text PDF

Source
http://bioinformatics.oxfordjournals.org/content/early/2012/
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
Publisher Site
http://dx.doi.org/10.1093/bioinformatics/bts669DOI Listing
January 2013