Publications

Publications

2020

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Intestinal transkingdom analysis on the impact of antibiotic perturbation in health and critical illness
Haak BW, Argelaguet R, Kinsella CM, Kullberg RF, Lankelma JM, Hakvoort TB, Hugenholtz F, Kostidis S, Giera M, de Jonge WJ, Schultz MJ, van Gool T, van der Poll T, de Vos WM, van den Hoek L, Wiersinga WJ. Preprint DOI: 10.1101/2020.06.25.171553
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Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
Jerber J, Seaton D, Cuomo A, Kumasaka N, Haldane J, Steer J, Patel M, Pearce D, Andersson M, Bonder M, Mountjoy E, Ghoussaini M, Lancaster M, Marioni J, Merkle F, Stegle O, Gaffney D, HipSci Consortium. Preprint DOI: 10.1101/2020.05.21.103820
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Publisher Correction: Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Garcia HD, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Nature genetics Volume 52 (2020) p.464 DOI: 10.1038/s41588-020-0598-1
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Minimal phenotyping yields genome-wide association signals of low specificity for major depression.
Cai N, Revez JA, Adams MJ, Andlauer TFM, Breen G, Byrne EM, Clarke TK, Forstner AJ, Grabe HJ, Hamilton SP, Levinson DF, Lewis CM, Lewis G, Martin NG, Milaneschi Y, Mors O, Müller-Myhsok B, Penninx BWJH, Perlis RH, Pistis G, Potash JB, Preisig M, Shi J, Smoller JW, Streit F, Tiemeier H, Uher R, Van der Auwera S, Viktorin A, Weissman MM, MDD Working Group of the Psychiatric Genomics Consortium, Kendler KS, Flint J. Nature genetics Volume 52 (2020) p.437-447 DOI: 10.1038/s41588-020-0594-5
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DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases.
Essack M, Salhi A, Van Neste C, Raies AB, Tifratene F, Uludag M, Hungler A, Zaric B, Zafirovic S, Gojobori T, Isenovic E, Bajic VP. Oxidative medicine and cellular longevity Volume 2020 (2020) p.5904315 DOI: 10.1155/2020/5904315
Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O. Nature communications Volume 11 (2020) p.1572 DOI: 10.1038/s41467-020-15098-y
Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes.
McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Lyu R, HipSci Consortium, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA. Nature methods Volume 17 (2020) p.414-421 DOI: 10.1038/s41592-020-0766-3
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The single-cell eQTLGen consortium.
van der Wijst M, de Vries DH, Groot HE, Trynka G, Hon CC, Bonder MJ, Stegle O, Nawijn MC, Idaghdour Y, van der Harst P, Ye CJ, Powell J, Theis FJ, Mahfouz A, Heinig M, Franke L. eLife Volume 9 (2020) DOI: 10.7554/elife.52155
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Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data.
Holland CH, Tanevski J, Perales-Patón J, Gleixner J, Kumar MP, Mereu E, Joughin BA, Stegle O, Lauffenburger DA, Heyn H, Szalai B, Saez-Rodriguez J. Genome biology Volume 21 (2020) p.36 DOI: 10.1186/s13059-020-1949-z
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression.
Cuomo ASE, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, HipSci Consortium, Vallier L, Marioni JC, Chhatriwala M, Stegle O. Nature communications Volume 11 (2020) p.810 DOI: 10.1038/s41467-020-14457-z
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Eleven grand challenges in single-cell data science.
Lähnemann D, Köster J, Szczurek E, McCarthy DJ, Hicks SC, Robinson MD, Vallejos CA, Campbell KR, Beerenwinkel N, Mahfouz A, Pinello L, Skums P, Stamatakis A, Attolini CS, Aparicio S, Baaijens J, Balvert M, Barbanson B, Cappuccio A, Corleone G, Dutilh BE, Florescu M, Guryev V, Holmer R, Jahn K, Lobo TJ, Keizer EM, Khatri I, Kielbasa SM, Korbel JO, Kozlov AM, Kuo TH, Lelieveldt BPF, Mandoiu II, Marioni JC, Marschall T, Mölder F, Niknejad A, Raczkowski L, Reinders M, Ridder J, Saliba AE, Somarakis A, Stegle O, Theis FJ, Yang H, Zelikovsky A, McHardy AC, Raphael BJ, Shah SP, Schönhuth A. Genome biology Volume 21 (2020) p.31 DOI: 10.1186/s13059-020-1926-6
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Freshwater monitoring by nanopore sequencing
Urban L, Holzer A, Baronas JJ, Hall M, Braeuninger-Weimer P, Scherm MJ, Kunz DJ, Perera SN, Martin-Herranz DE, Tipper ET, Salter SJ, Stammnitz MR. Preprint DOI: 10.1101/2020.02.06.936302
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Pan-cancer analysis of whole genomes.
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. Nature Volume 578 (2020) p.82-93 DOI: 10.1038/s41586-020-1969-6
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High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations.
Zhang Y, Chen F, Fonseca NA, He Y, Fujita M, Nakagawa H, Zhang Z, Brazma A, PCAWG Transcriptome Working Group, PCAWG Structural Variation Working Group, Creighton CJ, PCAWG Consortium. Nature communications Volume 11 (2020) p.736 DOI: 10.1038/s41467-019-13885-w
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Selecting likely causal risk factors from high-throughput experiments using multivariable Mendelian randomization.
Zuber V, Colijn JM, Klaver C, Burgess S. Nature communications Volume 11 (2020) p.29 DOI: 10.1038/s41467-019-13870-3

2019

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scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.
Madissoon E, Wilbrey-Clark A, Miragaia RJ, Saeb-Parsy K, Mahbubani KT, Georgakopoulos N, Harding P, Polanski K, Huang N, Nowicki-Osuch K, Fitzgerald RC, Loudon KW, Ferdinand JR, Clatworthy MR, Tsingene A, van Dongen S, Dabrowska M, Patel M, Stubbington MJT, Teichmann SA, Stegle O, Meyer KB. Genome biology Volume 21 (2019) p.1 DOI: 10.1186/s13059-019-1906-x
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Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma.
Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Nature genetics Volume 52 (2020) p.29-34 DOI: 10.1038/s41588-019-0547-z
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Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference.
Huang Y, McCarthy DJ, Stegle O. Genome biology Volume 20 (2019) p.273 DOI: 10.1186/s13059-019-1865-2
Multi-omics profiling of mouse gastrulation at single-cell resolution.
Argelaguet R, Clark SJ, Mohammed H, Stapel LC, Krueger C, Kapourani CA, Imaz-Rosshandler I, Lohoff T, Xiang Y, Hanna CW, Smallwood S, Ibarra-Soria X, Buettner F, Sanguinetti G, Xie W, Krueger F, Göttgens B, Rugg-Gunn PJ, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W. Nature Volume 576 (2019) p.487-491 DOI: 10.1038/s41586-019-1825-8
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Comparison Study of Computational Prediction Tools for Drug-Target Binding Affinities.
Thafar M, Raies AB, Albaradei S, Essack M, Bajic VB. Frontiers in chemistry Volume 7 (2019) p.782 DOI: 10.3389/fchem.2019.00782
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Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease.
D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA. eLife Volume 8 (2019) DOI: 10.7554/elife.48476
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MOFA+: a probabilistic framework for comprehensive integration of structured single-cell data
Argelaguet R, Arnol D, Bredikhin D, Deloro Y, Velten B, Marioni JC, Stegle O. Preprint DOI: 10.1101/837104
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Hematopoietic Npc1 mutation shifts gut microbiota composition in Ldlr-/- mice on a high-fat, high-cholesterol diet.
Houben T, Penders J, Oligschlaeger Y, Dos Reis IAM, Bonder MJ, Koonen DP, Fu J, Hofker MH, Shiri-Sverdlov R. Scientific reports Volume 9 (2019) p.14956 DOI: 10.1038/s41598-019-51525-x
Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis.
Arnol D, Schapiro D, Bodenmiller B, Saez-Rodriguez J, Stegle O. Cell reports Volume 29 (2019) p.202-211.e6 DOI: 10.1016/j.celrep.2019.08.077
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Systematic assessment of regulatory effects of human disease variants in pluripotent cells
Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D’Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Horta D, Smith EN, Frazer KA, Montgomery SB, Stegle O, HipSci Consortium, iPSCORE Consortium, GENESiPS Consortium, PhLiPS Consortium. Preprint DOI: 10.1101/784967
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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 Volume 178 (2019) p.1465-1477.e17 DOI: 10.1016/j.cell.2019.08.018
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 biology Volume 20 (2019) p.146 DOI: 10.1186/s13059-019-1753-9
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Genomic properties of structural variants and short tandem repeats that impact gene expression and complex traits in humans
Jakubosky D, D’Antonio M, Bonder MJ, Smail C, Donovan MK, Greenwald WWY, D’Antonio-Chronowska A, Matsui H, Stegle O, Smith EN, Montgomery SB, DeBoever C, Frazer KA, i2QTL Consortium. Preprint DOI: 10.1101/714477
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Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats
Jakubosky D, Smith EN, D’Antonio M, Bonder MJ, Greenwald WWY, D’Antonio-Chronowska A, Matsui H, Stegle O, Montgomery SB, DeBoever C, Frazer KA, i2QTL Consortium, HipSci Consortium. Preprint DOI: 10.1101/713198
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Mendelian randomization integrating GWAS and eQTL data reveals genetic determinants of complex and clinical traits.
Porcu E, Rüeger S, Lepik K, eQTLGen Consortium, BIOS Consortium, Santoni FA, Reymond A, Kutalik Z. Nature communications Volume 10 (2019) p.3300 DOI: 10.1038/s41467-019-10936-0
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Multi-omics Characterization of Interaction-mediated Control of Human Protein Abundance levels.
Sousa A, Gonçalves E, Mirauta B, Ochoa D, Stegle O, Beltrao P. Molecular & cellular proteomics : MCP Volume 18 (2019) p.S114-S125 DOI: 10.1074/mcp.ra118.001280
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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. Frontiers in molecular neuroscience Volume 12 (2019) p.139 DOI: 10.3389/fnmol.2019.00139
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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. Nature biotechnology Volume 37 (2019) p.592-600 DOI: 10.1038/s41587-019-0140-0
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Literature-Based Enrichment Insights into Redox Control of Vascular Biology.
Essack M, Salhi A, Stanimirovic J, Tifratene F, Bin Raies A, Hungler A, Uludag M, Van Neste C, Trpkovic A, Bajic VP, Bajic VB, Isenovic ER. Oxidative medicine and cellular longevity Volume 2019 (2019) p.1769437 DOI: 10.1155/2019/1769437
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Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
Cuomo AS, Seaton DD, McCarthy DJ, Martinez I, Bonder MJ, Garcia-Bernardo J, Amatya S, Madrigal P, Isaacson A, Buettner F, Knights A, Natarajan KN, Vallier L, Marioni JC, Chhatriwala M, Stegle O, HipSci Consortium. Preprint DOI: 10.1101/630996
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Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk.
Kurilshikov A, van den Munckhof ICL, Chen L, Bonder MJ, Schraa K, Rutten JHW, Riksen NP, de Graaf J, Oosting M, Sanna S, Joosten LAB, van der Graaf M, Brand T, Koonen DPY, van Faassen M, LifeLines DEEP Cohort Study, BBMRI Metabolomics Consortium, Slagboom PE, Xavier RJ, Kuipers F, Hofker MH, Wijmenga C, Netea MG, Zhernakova A, Fu J. Circulation research Volume 124 (2019) p.1808-1820 DOI: 10.1161/circresaha.118.314642
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Reverse GWAS: Using genetics to identify and model phenotypic subtypes.
Dahl A, Cai N, Ko A, Laakso M, Pajukanta P, Flint J, Zaitlen N. PLoS genetics Volume 15 (2019) p.e1008009 DOI: 10.1371/journal.pgen.1008009
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Epigenome-wide Association Study of Attention-Deficit/Hyperactivity Disorder Symptoms in Adults.
van Dongen J, Zilhão NR, Sugden K, BIOS Consortium, Hannon EJ, Mill J, Caspi A, Agnew-Blais J, Arseneault L, Corcoran DL, Moffitt TE, Poulton R, Franke B, Boomsma DI. Biological psychiatry Volume 86 (2019) p.599-607 DOI: 10.1016/j.biopsych.2019.02.016
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In-depth genetic analysis of 6p21.3 reveals insights into associations between HLA types and complex traits and disease
D’Antonio M, Reyna J, D’Antonio-Chronowska A, Bonder M, Jakubosky D, Matsui H, Smith EN, Stegle O, Nariai N, Frazer KA. Preprint DOI: 10.1101/564161
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 biology Volume 20 (2019) p.30 DOI: 10.1186/s13059-019-1644-0
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Screening for genes that accelerate the epigenetic ageing clock in humans reveals a role for the H3K36 methyltransferase NSD1
Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Stegle O, Sadikovic B, Reik W, Thornton JM. Preprint DOI: 10.1101/545830
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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 biology Volume 20 (2019) p.27 DOI: 10.1186/s13059-019-1637-z
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 reports Volume 26 (2019) p.2078-2087.e3 DOI: 10.1016/j.celrep.2019.01.094
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Single cell multi-omics profiling reveals a hierarchical epigenetic landscape during mammalian germ layer specification: Supplementary Figures
Argelaguet R, Mohammed H, Clark S, Stapel C, Krueger C, Kapourani CA, Xiang Y, Hanna C, Smallwood S, Ibarra Soria X, Buettner F, Sanguinetti G, Krueger F, Xie W, Rugg-Gunn P, Kelsey G, Dean W, Nichols J, Stegle O, Marioni JC, Reik W. Preprint DOI: 10.1101/519207
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Literature-Based Enrichment Insights into Redox Control of Vascular Biology
Essack M, Salhi A, Stanimirovic J, Tifratene F, Raies A, Hungler A, Uludag M, Neste CV, Trpkovic A, Bajic VP, Bajic VB, Isenovic ER. Oxidative medicine and cellular longevity Volume 2019 (2019) DOI: 10.1155/2019/1769437
Using BRIE to Detect and Analyze Splicing Isoforms in scRNA-Seq Data.
Huang Y, Sanguinetti G. Methods in molecular biology (Clifton, N.J.) Volume 1935 (2019) p.175-185 DOI: 10.1007/978-1-4939-9057-3_12

2018

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Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.
Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK. Science translational medicine Volume 10 (2018) DOI: 10.1126/scitranslmed.aap8914
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Association of Genetic Variants Related to Gluteofemoral vs Abdominal Fat Distribution With Type 2 Diabetes, Coronary Disease, and Cardiovascular Risk Factors.
Lotta LA, Wittemans LBL, Zuber V, Stewart ID, Sharp SJ, Luan J, Day FR, Li C, Bowker N, Cai L, De Lucia Rolfe E, Khaw KT, Perry JRB, O'Rahilly S, Scott RA, Savage DB, Burgess S, Wareham NJ, Langenberg C. JAMA Volume 320 (2018) p.2553-2563 DOI: 10.1001/jama.2018.19329
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Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.
Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J, LifeLines cohort study, BIOS consortium. Nature genetics Volume 50 (2018) p.1752 DOI: 10.1038/s41588-018-0275-9
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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. Nature genetics Volume 51 (2019) p.180-186 DOI: 10.1038/s41588-018-0271-0
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Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles.
Sinha T, Vich Vila A, Garmaeva S, Jankipersadsing SA, Imhann F, Collij V, Bonder MJ, Jiang X, Gurry T, Alm EJ, D'Amato M, Weersma RK, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A. Gut microbes Volume 10 (2019) p.358-366 DOI: 10.1080/19490976.2018.1528822
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Unraveling the polygenic architecture of complex traits using blood eQTL metaanalysis
Võsa U, Claringbould A, Westra H, Bonder MJ, Deelen P, Zeng B, Kirsten H, Saha A, Kreuzhuber R, Kasela S, Pervjakova N, Alvaes I, Fave M, Agbessi M, Christiansen M, Jansen R, Seppälä I, Tong L, Teumer A, Schramm K, Hemani G, Verlouw J, Yaghootkar H, Sönmez R, Brown A, Kukushkina V, Kalnapenkis A, Rüeger S, Porcu E, Kronberg-Guzman J, Kettunen J, Powell J, Lee B, Zhang F, Arindrarto W, Beutner F, Brugge H, Dmitreva J, Elansary M, Fairfax BP, Georges M, Heijmans BT, Kähönen M, Kim Y, Knight JC, Kovacs P, Krohn K, Li S, Loeffler M, Marigorta UM, Mei H, Momozawa Y, Müller-Nurasyid M, Nauck M, Nivard M, Penninx B, Pritchard J, Raitakari O, Rotzchke O, Slagboom EP, Stehouwer CD, Stumvoll M, Sullivan P, Hoen PA‘, Thiery J, Tönjes A, van Dongen J, van Iterson M, Veldink J, Völker U, Wijmenga C, Swertz M, Andiappan A, Montgomery GW, Ripatti S, Perola M, Kutalik Z, Dermitzakis E, Bergmann S, Frayling T, van Meurs J, Prokisch H, Ahsan H, Pierce B, Lehtimäki T, Boomsma D, Psaty BM, Gharib SA, Awadalla P, Milani L, Ouwehand W, Downes K, Stegle O, Battle A, Yang J, Visscher PM, Scholz M, Gibson G, Esko T, Franke L, BIOS Consortium, i2QTL Consortium. Preprint DOI: 10.1101/447367
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Population-scale proteome variation in human induced pluripotent stem cells
Mirauta BA, Seaton DD, Bensaddek D, Brenes A, Bonder MJ, Kilpinen H, Stegle O, Lamond AI, HipSci Consortium. Preprint DOI: 10.1101/439216
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Metabolic regulation of pluripotency and germ cell fate through α-ketoglutarate.
Tischler J, Gruhn WH, Reid J, Allgeyer E, Buettner F, Marr C, Theis F, Simons BD, Wernisch L, Surani MA. The EMBO journal Volume 38 (2019) DOI: 10.15252/embj.201899518
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Dawn and photoperiod sensing by phytochrome A.
Seaton DD, Toledo-Ortiz G, Ganpudi A, Kubota A, Imaizumi T, Halliday KJ. Proceedings of the National Academy of Sciences of the United States of America Volume 115 (2018) p.10523-10528 DOI: 10.1073/pnas.1803398115
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Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome.
Zhernakova DV, Le TH, Kurilshikov A, Atanasovska B, Bonder MJ, Sanna S, Claringbould A, Võsa U, Deelen P, Franke L, de Boer RA, Kuipers F, Netea MG, Hofker MH, Wijmenga C, Zhernakova A, Fu J, LifeLines cohort study, BIOS consortium. Nature genetics Volume 50 (2018) p.1524-1532 DOI: 10.1038/s41588-018-0224-7
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Cardelino: Integrating whole exomes and single-cell transcriptomes to reveal phenotypic impact of somatic variants
McCarthy DJ, Rostom R, Huang Y, Kunz DJ, Danecek P, Bonder MJ, Hagai T, Wang W, Gaffney DJ, Simons BD, Stegle O, Teichmann SA, HipSci Consortium. Preprint DOI: 10.1101/413047
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Cross-tissue eQTL enrichment of associations in schizophrenia.
Bettella F, Brown AA, Smeland OB, Wang Y, Witoelar A, Buil Demur AA, Thompson WK, Zuber V, Dale AM, Djurovic S, Andreassen OA. PloS one Volume 13 (2018) p.e0202812 DOI: 10.1371/journal.pone.0202812
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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. Nature communications Volume 9 (2018) p.3385 DOI: 10.1038/s41467-018-05811-3
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Selecting causal risk factors from high-throughput experiments using multivariable Mendelian randomization
Zuber V, Colijn JM, Klaver C, Burgess S. Preprint DOI: 10.1101/396333
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Genome-wide identification of directed gene networks using large-scale population genomics data.
Luijk R, Dekkers KF, van Iterson M, Arindrarto W, Claringbould A, Hop P, Boomsma DI, van Duijn CM, van Greevenbroek MMJ, Veldink JH, Wijmenga C, Franke L, 't Hoen PAC, Jansen R, van Meurs J, Mei H, Slagboom PE, Heijmans BT, van Zwet EW, BIOS (Biobank-based Integrative Omics Study) Consortium. Nature communications Volume 9 (2018) p.3097 DOI: 10.1038/s41467-018-05452-6
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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 Volume 34 (2018) p.211-224.e6 DOI: 10.1016/j.ccell.2018.07.001
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Modal-based estimation via heterogeneity-penalized weighting: model averaging for consistent and efficient estimation in Mendelian randomization when a plurality of candidate instruments are valid.
Burgess S, Zuber V, Gkatzionis A, Foley CN. International journal of epidemiology Volume 47 (2018) p.1242-1254 DOI: 10.1093/ije/dyy080
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Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes.
Xue A, Wu Y, Zhu Z, Zhang F, Kemper KE, Zheng Z, Yengo L, Lloyd-Jones LR, Sidorenko J, Wu Y, eQTLGen Consortium, McRae AF, Visscher PM, Zeng J, Yang J. Nature communications Volume 9 (2018) p.2941 DOI: 10.1038/s41467-018-04951-w
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Kipoi: accelerating the 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, Urban L, Kundaje A, Stegle O, Gagneur J. Preprint DOI: 10.1101/375345
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A High-Resolution Genetic Map for the Laboratory Rat.
Littrell J, Tsaih SW, Baud A, Rastas P, Solberg-Woods L, Flister MJ. G3 (Bethesda, Md.) Volume 8 (2018) p.2241-2248 DOI: 10.1534/g3.118.200187
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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 systems Volume 7 (2018) p.63-76.e12 DOI: 10.1016/j.cels.2018.06.012
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A correction for sample overlap in genome-wide association studies in a polygenic pleiotropy-informed framework.
LeBlanc M, Zuber V, Thompson WK, Andreassen OA, Schizophrenia and Bipolar Disorder Working Groups of the Psychiatric Genomics Consortium, Frigessi A, Andreassen BK. BMC genomics Volume 19 (2018) p.494 DOI: 10.1186/s12864-018-4859-7
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. Molecular systems biology Volume 14 (2018) p.e8124 DOI: 10.15252/msb.20178124
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Combined single-cell profiling of expression and DNA methylation reveals splicing regulation and heterogeneity
Linker SM, Urban L, Clark S, Chhatriwala M, Amatya S, McCarthy DJ, Ebersberger I, Vallier L, Reik W, Stegle O, Bonder MJ. Preprint DOI: 10.1101/328138
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Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.
Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, Blackwood DRH, Bryois J, Buttenschøn HN, Bybjerg-Grauholm J, Cai N, Castelao E, Christensen JH, Clarke TK, Coleman JIR, Colodro-Conde L, Couvy-Duchesne B, Craddock N, Crawford GE, Crowley CA, Dashti HS, Davies G, Deary IJ, Degenhardt F, Derks EM, Direk N, Dolan CV, Dunn EC, Eley TC, Eriksson N, Escott-Price V, Kiadeh FHF, Finucane HK, Forstner AJ, Frank J, Gaspar HA, Gill M, Giusti-Rodríguez P, Goes FS, Gordon SD, Grove J, Hall LS, Hannon E, Hansen CS, Hansen TF, Herms S, Hickie IB, Hoffmann P, Homuth G, Horn C, Hottenga JJ, Hougaard DM, Hu M, Hyde CL, Ising M, Jansen R, Jansen R, Jin F, Jorgenson E, Knowles JA, Kohane IS, Kraft J, Kretzschmar WW, Krogh J, Kutalik Z, Lane JM, Li Y, Li Y, Lind PA, Liu X, Lu L, MacIntyre DJ, MacKinnon DF, Maier RM, Maier W, Marchini J, Mbarek H, McGrath P, McGuffin P, Medland SE, Mehta D, Middeldorp CM, Mihailov E, Milaneschi Y, Milani L, Mill J, Mondimore FM, Montgomery GW, Mostafavi S, Mullins N, Nauck M, Ng B, Nivard MG, Nyholt DR, O'Reilly PF, Oskarsson H, Owen MJ, Painter JN, Pedersen CB, Pedersen MG, Peterson RE, Pettersson E, Peyrot WJ, Pistis G, Posthuma D, Purcell SM, Quiroz JA, Qvist P, Rice JP, Riley BP, Rivera M, Saeed Mirza S, Saxena R, Schoevers R, Schulte EC, Shen L, Shi J, Shyn SI, Sigurdsson E, Sinnamon GBC, Smit JH, Smith DJ, Stefansson H, Steinberg S, Stockmeier CA, Streit F, Strohmaier J, Tansey KE, Teismann H, Teumer A, Thompson W, Thomson PA, Thorgeirsson TE, Tian C, Traylor M, Treutlein J, Trubetskoy V, Uitterlinden AG, Umbricht D, Van der Auwera S, van Hemert AM, Viktorin A, Visscher PM, Wang Y, Webb BT, Weinsheimer SM, Wellmann J, Willemsen G, Witt SH, Wu Y, Xi HS, Yang J, Zhang F, eQTLGen, 23andMe, Arolt V, Baune BT, Berger K, Boomsma DI, Cichon S, Dannlowski U, de Geus ECJ, DePaulo JR, Domenici E, Domschke K, Esko T, Grabe HJ, Hamilton SP, Hayward C, Heath AC, Hinds DA, Kendler KS, Kloiber S, Lewis G, Li QS, Lucae S, Madden PFA, Magnusson PK, Martin NG, McIntosh AM, Metspalu A, Mors O, Mortensen PB, Müller-Myhsok B, Nordentoft M, Nöthen MM, O'Donovan MC, Paciga SA, Pedersen NL, Penninx BWJH, Perlis RH, Porteous DJ, Potash JB, Preisig M, Rietschel M, Schaefer C, Schulze TG, Smoller JW, Stefansson K, Tiemeier H, Uher R, Völzke H, Weissman MM, Werge T, Winslow AR, Lewis CM, Levinson DF, Breen G, Børglum AD, Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium. Nature genetics Volume 50 (2018) p.668-681 DOI: 10.1038/s41588-018-0090-3
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Inferring Causal Relationships Between Risk Factors and Outcomes from Genome-Wide Association Study Data.
Burgess S, Foley CN, Zuber V. Annual review of genomics and human genetics Volume 19 (2018) p.303-327 DOI: 10.1146/annurev-genom-083117-021731
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Dissecting the mechanisms underlying indirect genetic effects on biomedical phenotypes: a study of 170 behavioural, physiological and morphological phenotypes measured in adult laboratory mice
Baud A, Casale FP, Nicod J, Stegle O. Preprint DOI: 10.1101/302349
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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 Volume 13 (2018) p.e0195788 DOI: 10.1371/journal.pone.0195788
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Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime
Noordally ZB, Hindle MM, Martin SF, Seaton DD, Simpson TI, Bihan TL, Millar AJ. Preprint DOI: 10.1101/287862
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SpatialDE: identification of spatially variable genes.
Svensson V, Teichmann SA, Stegle O. Nature methods Volume 15 (2018) p.343-346 DOI: 10.1038/nmeth.4636
Molecular Genetic Analysis Subdivided by Adversity Exposure Suggests Etiologic Heterogeneity in Major Depression.
Peterson RE, Cai N, Dahl AW, Bigdeli TB, Edwards AC, Webb BT, Bacanu SA, Zaitlen N, Flint J, Kendler KS. The American journal of psychiatry Volume 175 (2018) p.545-554 DOI: 10.1176/appi.ajp.2017.17060621
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Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism.
Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W. Molecular systems biology Volume 14 (2018) p.e7962 DOI: 10.15252/msb.20177962
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DNA methylation in childhood asthma: an epigenome-wide meta-analysis.
Xu CJ, Söderhäll C, Bustamante M, Baïz N, Gruzieva O, Gehring U, Mason D, Chatzi L, Basterrechea M, Llop S, Torrent M, Forastiere F, Fantini MP, Carlsen KCL, Haahtela T, Morin A, Kerkhof M, Merid SK, van Rijkom B, Jankipersadsing SA, Bonder MJ, Ballereau S, Vermeulen CJ, Aguirre-Gamboa R, de Jongste JC, Smit HA, Kumar A, Pershagen G, Guerra S, Garcia-Aymerich J, Greco D, Reinius L, McEachan RRC, Azad R, Hovland V, Mowinckel P, Alenius H, Fyhrquist N, Lemonnier N, Pellet J, Auffray C, BIOS Consortium, van der Vlies P, van Diemen CC, Li Y, Wijmenga C, Netea MG, Moffatt MF, Cookson WOCM, Anto JM, Bousquet J, Laatikainen T, Laprise C, Carlsen KH, Gori D, Porta D, Iñiguez C, Bilbao JR, Kogevinas M, Wright J, Brunekreef B, Kere J, Nawijn MC, Annesi-Maesano I, Sunyer J, Melén E, Koppelman GH. The Lancet. Respiratory medicine Volume 6 (2018) p.379-388 DOI: 10.1016/s2213-2600(18)30052-3
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A linear mixed model approach to study multivariate gene-environment interactions
Moore R, Casale FP, Bonder MJ, Horta D, Franke L, Barroso I, Stegle O, BIOS Consortium. Preprint DOI: 10.1101/270611
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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. Nature communications Volume 9 (2018) p.781 DOI: 10.1038/s41467-018-03149-4
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Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT
Kinmonth-Schultz HA, MacEwen MJ, Seaton DD, Millar AJ, Imaizumi T, Kim S. Preprint DOI: 10.1101/267104
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Detection of stable community structures within gut microbiota co-occurrence networks from different human populations.
Jackson MA, Bonder MJ, Kuncheva Z, Zierer J, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Bell JT, Spector TD, Steves CJ. PeerJ Volume 6 (2018) p.e4303 DOI: 10.7717/peerj.4303
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A SNP panel for identification of DNA and RNA specimens.
Yousefi S, Abbassi-Daloii T, Kraaijenbrink T, Vermaat M, Mei H, van 't Hof P, van Iterson M, Zhernakova DV, Claringbould A, Franke L, 't Hart LM, Slieker RC, van der Heijden A, de Knijff P, BIOS consortium, 't Hoen PAC. BMC genomics Volume 19 (2018) p.90 DOI: 10.1186/s12864-018-4482-7
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Dawn and photoperiod sensing by phytochrome A
Seaton DD, Toledo-Ortiz G, Kubota A, Ganpudi A, Imaizumi T, Halliday KJ. Preprint DOI: 10.1101/253989
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Identification of shared genetic variants between schizophrenia and lung cancer.
Zuber V, Jönsson EG, Frei O, Witoelar A, Thompson WK, Schork AJ, Bettella F, Wang Y, Djurovic S, Smeland OB, Dieset I, Fanous AH, Desikan RS, Küry S, Bézieau S, Dale AM, Mills IG, Andreassen OA. Scientific reports Volume 8 (2018) p.674 DOI: 10.1038/s41598-017-16481-4
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Polygenic hazard score to guide screening for aggressive prostate cancer: development and validation in large scale cohorts.
Seibert TM, Fan CC, Wang Y, Zuber V, Karunamuni R, Parsons JK, Eeles RA, Easton DF, Kote-Jarai Z, Al Olama AA, Garcia SB, Muir K, Grönberg H, Wiklund F, Aly M, Schleutker J, Sipeky C, Tammela TL, Nordestgaard BG, Nielsen SF, Weischer M, Bisbjerg R, Røder MA, Iversen P, Key TJ, Travis RC, Neal DE, Donovan JL, Hamdy FC, Pharoah P, Pashayan N, Khaw KT, Maier C, Vogel W, Luedeke M, Herkommer K, Kibel AS, Cybulski C, Wokolorczyk D, Kluzniak W, Cannon-Albright L, Brenner H, Cuk K, Saum KU, Park JY, Sellers TA, Slavov C, Kaneva R, Mitev V, Batra J, Clements JA, Spurdle A, Teixeira MR, Paulo P, Maia S, Pandha H, Michael A, Kierzek A, Karow DS, Mills IG, Andreassen OA, Dale AM, PRACTICAL Consortium*. BMJ (Clinical research ed.) Volume 360 (2018) p.j5757 DOI: 10.1136/bmj.j5757
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 research Volume 46 (2018) p.D246-D251 DOI: 10.1093/nar/gkx1158

2017

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Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast.
Aslanzadeh V, Huang Y, Sanguinetti G, Beggs JD. Genome research Volume 28 (2018) p.203-213 DOI: 10.1101/gr.225615.117
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Molecular and functional variation in iPSC-derived sensory neurons.
Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, HIPSCI Consortium, Gutteridge A, Gaffney DJ. Nature genetics Volume 50 (2018) p.54-61 DOI: 10.1038/s41588-017-0005-8
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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 Volume 6 (2017) DOI: 10.7554/elife.27041
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DNA Methylation Analysis Identifies Loci for Blood Pressure Regulation.
Richard MA, Huan T, Ligthart S, Gondalia R, Jhun MA, Brody JA, Irvin MR, Marioni R, Shen J, Tsai PC, Montasser ME, Jia Y, Syme C, Salfati EL, Boerwinkle E, Guan W, Mosley TH, Bressler J, Morrison AC, Liu C, Mendelson MM, Uitterlinden AG, van Meurs JB, BIOS Consortium, Franco OH, Zhang G, Li Y, Stewart JD, Bis JC, Psaty BM, Chen YI, Kardia SLR, Zhao W, Turner ST, Absher D, Aslibekyan S, Starr JM, McRae AF, Hou L, Just AC, Schwartz JD, Vokonas PS, Menni C, Spector TD, Shuldiner A, Damcott CM, Rotter JI, Palmas W, Liu Y, Paus T, Horvath S, O'Connell JR, Guo X, Pausova Z, Assimes TL, Sotoodehnia N, Smith JA, Arnett DK, Deary IJ, Baccarelli AA, Bell JT, Whitsel E, Dehghan A, Levy D, Fornage M. American journal of human genetics Volume 101 (2017) p.888-902 DOI: 10.1016/j.ajhg.2017.09.028
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Assessing the Gene Regulatory Landscape in 1,188 Human Tumors
Calabrese C, Lehmann K, Urban L, Liu F, Erkek S, Fonseca N, Kahles A, Kilpinen H, Markowski J, Waszak S, Korbel J, Zhang Z, Brazma A, Rätsch G, Schwarz R, Stegle O, PCAWG Group 3. Preprint DOI: 10.1101/225441
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DNA methylation markers associated with type 2 diabetes, fasting glucose and HbA1c levels: a systematic review and replication in a case-control sample of the Lifelines study.
Walaszczyk E, Luijten M, Spijkerman AMW, Bonder MJ, Lutgers HL, Snieder H, Wolffenbuttel BHR, van Vliet-Ostaptchouk JV. Diabetologia Volume 61 (2018) p.354-368 DOI: 10.1007/s00125-017-4497-7
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DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development.
Kraiczy J, Nayak KM, Howell KJ, Ross A, Forbester J, Salvestrini C, Mustata R, Perkins S, Andersson-Rolf A, Leenen E, Liebert A, Vallier L, Rosenstiel PC, Stegle O, Dougan G, Heuschkel R, Koo BK, Zilbauer M. Gut Volume 68 (2019) p.49-61 DOI: 10.1136/gutjnl-2017-314817
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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. Nature communications Volume 8 (2017) p.1511 DOI: 10.1038/s41467-017-01818-4
f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.
Buettner F, Pratanwanich N, McCarthy DJ, Marioni JC, Stegle O. Genome biology Volume 18 (2017) p.212 DOI: 10.1186/s13059-017-1334-8
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An epigenome-wide association study meta-analysis of educational attainment.
Karlsson Linnér R, Marioni RE, Rietveld CA, Simpkin AJ, Davies NM, Watanabe K, Armstrong NJ, Auro K, Baumbach C, Bonder MJ, Buchwald J, Fiorito G, Ismail K, Iurato S, Joensuu A, Karell P, Kasela S, Lahti J, McRae AF, Mandaviya PR, Seppälä I, Wang Y, Baglietto L, Binder EB, Harris SE, Hodge AM, Horvath S, Hurme M, Johannesson M, Latvala A, Mather KA, Medland SE, Metspalu A, Milani L, Milne RL, Pattie A, Pedersen NL, Peters A, Polidoro S, Räikkönen K, Severi G, Starr JM, Stolk L, Waldenberger M, Eriksson JG, Esko T, Franke L, Gieger C, Giles GG, Hägg S, Jousilahti P, Kaprio J, Kähönen M, Lehtimäki T, Martin NG, van Meurs JBC, Ollikainen M, Perola M, Posthuma D, Raitakari OT, Sachdev PS, Taskesen E, Uitterlinden AG, Vineis P, Wijmenga C, Wright MJ, Relton C, Davey Smith G, Deary IJ, Deary IJ, Koellinger PD, Benjamin DJ. Molecular psychiatry Volume 22 (2017) p.1680-1690 DOI: 10.1038/mp.2017.210
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Genetically defined elevated homocysteine levels do not result in widespread changes of DNA methylation in leukocytes.
Mandaviya PR, Joehanes R, Aïssi D, Kühnel B, Marioni RE, Truong V, Stolk L, Beekman M, Bonder MJ, Franke L, Gieger C, Huan T, Ikram MA, Kunze S, Liang L, Lindemans J, Liu C, McRae AF, Mendelson MM, Müller-Nurasyid M, Peters A, Slagboom PE, Starr JM, Trégouët DA, Uitterlinden AG, van Greevenbroek MMJ, van Heemst D, van Iterson M, Wells PS, Yao C, Deary IJ, Gagnon F, Heijmans BT, Levy D, Morange PE, Waldenberger M, Heil SG, van Meurs JBJ, CHARGE Consortium Epigenetics group and BIOS Consortium. PloS one Volume 12 (2017) p.e0182472 DOI: 10.1371/journal.pone.0182472
DNA Methylation and Transcription Patterns in Intestinal Epithelial Cells From Pediatric Patients With Inflammatory Bowel Diseases Differentiate Disease Subtypes and Associate With Outcome.
Howell KJ, Kraiczy J, Nayak KM, Gasparetto M, Ross A, Lee C, Mak TN, Koo BK, Kumar N, Lawley T, Sinha A, Rosenstiel P, Heuschkel R, Stegle O, Zilbauer M. Gastroenterology Volume 154 (2018) p.585-598 DOI: 10.1053/j.gastro.2017.10.007
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Single-cell epigenomics: Recording the past and predicting the future.
Kelsey G, Stegle O, Reik W. Science (New York, N.Y.) Volume 358 (2017) p.69-75 DOI: 10.1126/science.aan6826
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Mendelian randomization with fine-mapped genetic data: Choosing from large numbers of correlated instrumental variables.
Burgess S, Zuber V, Valdes-Marquez E, Sun BB, Hopewell JC. Genetic epidemiology Volume 41 (2017) p.714-725 DOI: 10.1002/gepi.22077
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C-reactive protein upregulates the whole blood expression of CD59 - an integrative analysis.
Lepik K, Annilo T, Kukuškina V, eQTLGen Consortium, Kisand K, Kutalik Z, Peterson P, Peterson H. PLoS computational biology Volume 13 (2017) p.e1005766 DOI: 10.1371/journal.pcbi.1005766
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Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
PCAWG Transcriptome Core Group, Calabrese C, Davidson NR, Fonseca NA, He Y, Kahles A, Lehmann K, Liu F, Shiraishi Y, Soulette CM, Urban L, Demircioğlu D, Greger L, Li S, Liu D, Perry MD, Xiang L, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BF, Wu K, Yang H, Brazma A, Brooks AN, Göke J, Rätsch G, Schwarz RF, Stegle O, Zhang Z, PCAWG Transcriptome Working Group, ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/183889
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Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
Seaton DD, Graf A, Baerenfaller K, Stitt M, Millar AJ, Gruissem W. Preprint DOI: 10.1101/182071
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A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters
Demircioğlu D, Kindermans M, Nandi T, Cukuroglu E, Calabrese C, Fonseca NA, Kahles A, Lehmann K, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J, on behalf of the PCAWG Transcriptome Working Group, and the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Network. Preprint DOI: 10.1101/176487
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Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.
Roumeliotis TI, Williams SP, Gonçalves E, Alsinet C, Del Castillo Velasco-Herrera M, Aben N, Ghavidel FZ, Michaut M, Schubert M, Price S, Wright JC, Yu L, Yang M, Dienstmann R, Guinney J, Beltrao P, Brazma A, Pardo M, Stegle O, Adams DJ, Wessels L, Saez-Rodriguez J, McDermott U, Choudhary JS. Cell reports Volume 20 (2017) p.2201-2214 DOI: 10.1016/j.celrep.2017.08.010
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Platelet function is modified by common sequence variation in megakaryocyte super enhancers.
Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M. Nature communications Volume 8 (2017) p.16058 DOI: 10.1038/ncomms16058
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BRIE: transcriptome-wide splicing quantification in single cells.
Huang Y, Sanguinetti G. Genome biology Volume 18 (2017) p.123 DOI: 10.1186/s13059-017-1248-5
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Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Nature Volume 546 (2017) p.686 DOI: 10.1038/nature23012
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SpatialDE - Identification of spatially variable genes
Svensson V, Teichmann SA, Stegle O. Preprint DOI: 10.1101/143321
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Whole-Genome Sequencing Coupled to Imputation Discovers Genetic Signals for Anthropometric Traits.
Tachmazidou I, Süveges D, Min JL, Ritchie GRS, Steinberg J, Walter K, Iotchkova V, Schwartzentruber J, Huang J, Memari Y, McCarthy S, Crawford AA, Bombieri C, Cocca M, Farmaki AE, Gaunt TR, Jousilahti P, Kooijman MN, Lehne B, Malerba G, Männistö S, Matchan A, Medina-Gomez C, Metrustry SJ, Nag A, Ntalla I, Paternoster L, Rayner NW, Sala C, Scott WR, Shihab HA, Southam L, St Pourcain B, Traglia M, Trajanoska K, Zaza G, Zhang W, Artigas MS, Bansal N, Benn M, Chen Z, Danecek P, Lin WY, Locke A, Luan J, Manning AK, Mulas A, Sidore C, Tybjaerg-Hansen A, Varbo A, Zoledziewska M, Finan C, Hatzikotoulas K, Hendricks AE, Kemp JP, Moayyeri A, Panoutsopoulou K, Szpak M, Wilson SG, Boehnke M, Cucca F, Di Angelantonio E, Langenberg C, Lindgren C, McCarthy MI, Morris AP, Nordestgaard BG, Scott RA, Tobin MD, Wareham NJ, SpiroMeta Consortium, GoT2D Consortium, Burton P, Chambers JC, Smith GD, Dedoussis G, Felix JF, Franco OH, Gambaro G, Gasparini P, Hammond CJ, Hofman A, Jaddoe VWV, Kleber M, Kooner JS, Perola M, Relton C, Ring SM, Rivadeneira F, Salomaa V, Spector TD, Stegle O, Toniolo D, Uitterlinden AG, arcOGEN Consortium, Understanding Society Scientific Group, UK10K Consortium, Barroso I, Greenwood CMT, Perry JRB, Walker BR, Butterworth AS, Xue Y, Durbin R, Small KS, Soranzo N, Timpson NJ, Zeggini E. American journal of human genetics Volume 100 (2017) p.865-884 DOI: 10.1016/j.ajhg.2017.04.014
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Reevaluation of SNP heritability in complex human traits.
Speed D, Cai N, UCLEB Consortium, Johnson MR, Nejentsev S, Balding DJ. Nature genetics Volume 49 (2017) p.986-992 DOI: 10.1038/ng.3865
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scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells
Clark SJ, Argelaguet R, Kapourani C, Stubbs TM, Lee HJ, Alda-Catalinas C, Krueger F, Sanguinetti G, Kelsey G, Marioni JC, Stegle O, Reik W. Preprint DOI: 10.1101/138685
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Parotid gland mean dose as a xerostomia predictor in low-dose domains.
Gabryś HS, Buettner F, Sterzing F, Hauswald H, Bangert M. Acta oncologica (Stockholm, Sweden) Volume 56 (2017) p.1197-1203 DOI: 10.1080/0284186x.2017.1324209
Erratum to: DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O. Genome biology Volume 18 (2017) p.90 DOI: 10.1186/s13059-017-1233-z
Common genetic variation drives molecular heterogeneity in human iPSCs.
Kilpinen H, Goncalves A, Leha A, Afzal V, Alasoo K, Ashford S, Bala S, Bensaddek D, Casale FP, Culley OJ, Danecek P, Faulconbridge A, Harrison PW, Kathuria A, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Mann A, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, White A, Patel SR, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Nature Volume 546 (2017) p.370-375 DOI: 10.1038/nature22403
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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, 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, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N, the Human Cell Atlas Meeting Participants. Preprint DOI: 10.1101/121202
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Vitamin A-Retinoic Acid Signaling Regulates Hematopoietic Stem Cell Dormancy.
Cabezas-Wallscheid N, Buettner F, Sommerkamp P, Klimmeck D, Ladel L, Thalheimer FB, Pastor-Flores D, Roma LP, Renders S, Zeisberger P, Przybylla A, Schönberger K, Scognamiglio R, Altamura S, Florian CM, Fawaz M, Vonficht D, Tesio M, Collier P, Pavlinic D, Geiger H, Schroeder T, Benes V, Dick TP, Rieger MA, Stegle O, Trumpp A. Cell Volume 169 (2017) p.807-823.e19 DOI: 10.1016/j.cell.2017.04.018
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Identification of Gene Loci That Overlap Between Schizophrenia and Educational Attainment.
Le Hellard S, Wang Y, Witoelar A, Zuber V, Bettella F, Hugdahl K, Espeseth T, Steen VM, Melle I, Desikan R, Schork AJ, Thompson WK, Dale AM, Djurovic S, Andreassen OA, Schizophrenia Working Group of the Psychiatric Genomics Consortium. Schizophrenia bulletin Volume 43 (2017) p.654-664 DOI: 10.1093/schbul/sbw085
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Tracking the Evolution of Non-Small-Cell Lung Cancer.
Jamal-Hanjani M, Wilson GA, McGranahan N, Birkbak NJ, Watkins TBK, Veeriah S, Shafi S, Johnson DH, Mitter R, Rosenthal R, Salm M, Horswell S, Escudero M, Matthews N, Rowan A, Chambers T, Moore DA, Turajlic S, Xu H, Lee SM, Forster MD, Ahmad T, Hiley CT, Abbosh C, Falzon M, Borg E, Marafioti T, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Shah R, Joseph L, Quinn AM, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Dentro S, Taniere P, O'Sullivan B, Lowe HL, Hartley JA, Iles N, Bell H, Ngai Y, Shaw JA, Herrero J, Szallasi Z, Schwarz RF, Stewart A, Quezada SA, Le Quesne J, Van Loo P, Dive C, Hackshaw A, Swanton C, TRACERx Consortium. The New England journal of medicine Volume 376 (2017) p.2109-2121 DOI: 10.1056/nejmoa1616288
Joint genetic analysis using variant sets reveals polygenic gene-context interactions.
Casale FP, Horta D, Rakitsch B, Stegle O. PLoS genetics Volume 13 (2017) p.e1006693 DOI: 10.1371/journal.pgen.1006693
DeepCpG: accurate prediction of single-cell DNA methylation states using deep learning.
Angermueller C, Lee HJ, Reik W, Stegle O, Stegle O. Genome biology Volume 18 (2017) p.67 DOI: 10.1186/s13059-017-1189-z
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Multi-tissue DNA methylation age predictor in mouse.
Stubbs TM, Bonder MJ, Stark AK, Krueger F, BI Ageing Clock Team, von Meyenn F, Stegle O, Reik W. Genome biology Volume 18 (2017) p.68 DOI: 10.1186/s13059-017-1203-5
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Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution.
Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Marie Quinn A, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, TRACERx consortium, PEACE consortium, Swanton C. Nature Volume 545 (2017) p.446-451 DOI: 10.1038/nature22364
Identifying genes for neurobehavioural traits in rodents: progress and pitfalls.
Baud A, Flint J. Disease models & mechanisms Volume 10 (2017) p.373-383 DOI: 10.1242/dmm.027789
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R.
McCarthy DJ, Campbell KR, Lun AT, Wills QF. Bioinformatics (Oxford, England) Volume 33 (2017) p.1179-1186 DOI: 10.1093/bioinformatics/btw777
Bromodomain protein 4 discriminates tissue-specific super-enhancers containing disease-specific susceptibility loci in prostate and breast cancer.
Zuber V, Bettella F, Witoelar A, PRACTICAL Consortium, CRUK GWAS, BCAC Consortium, TRICL Consortium, Andreassen OA, Mills IG, Urbanucci A. BMC genomics Volume 18 (2017) p.270 DOI: 10.1186/s12864-017-3620-y
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Multi-tissue DNA methylation age predictor in mouse
Stubbs TM, Bonder MJ, Stark A, Krueger F, von Meyenn F, Stegle O, Reik W, Clock Team BI Ageing. Preprint DOI: 10.1101/119206
Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MS, Fogg LG, Nair AS, Liligeto U, Stubbington MJ, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Science immunology Volume 2 (2017) DOI: 10.1126/sciimmunol.aal2192
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Prospective identification of hematopoietic lineage choice by deep learning.
Buggenthin F, Buettner F, Hoppe PS, Endele M, Kroiss M, Strasser M, Schwarzfischer M, Loeffler D, Kokkaliaris KD, Hilsenbeck O, Schroeder T, Theis FJ, Marr C. Nature methods Volume 14 (2017) p.403-406 DOI: 10.1038/nmeth.4182
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11,670 whole-genome sequences representative of the Han Chinese population from the CONVERGE project.
Cai N, Bigdeli TB, Kretzschmar WW, Li Y, Liang J, Hu J, Peterson RE, Bacanu S, Webb BT, Riley B, Li Q, Marchini J, Mott R, Kendler KS, Flint J. Scientific data Volume 4 (2017) p.170011 DOI: 10.1038/sdata.2017.11
Promoter shape varies across populations and affects promoter evolution and expression noise.
Schor IE, Degner JF, Harnett D, Cannavò E, Casale FP, Shim H, Garfield DA, Birney E, Stephens M, Stegle O, Furlong EE. Nature genetics Volume 49 (2017) p.550-558 DOI: 10.1038/ng.3791
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Genomic Rearrangements in Arabidopsis Considered as Quantitative Traits.
Imprialou M, Kahles A, Steffen JG, Osborne EJ, Gan X, Lempe J, Bhomra A, Belfield E, Visscher A, Greenhalgh R, Harberd NP, Goram R, Hein J, Robert-Seilaniantz A, Jones J, Stegle O, Kover P, Tsiantis M, Nordborg M, Rätsch G, Clark RM, Mott R. Genetics Volume 205 (2017) p.1425-1441 DOI: 10.1534/genetics.116.192823
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Linking circadian time to growth rate quantitatively via carbon metabolism
Chew YH, Seaton DD, Mengin V, Flis A, Mugford ST, Smith AM, Stitt M, Millar AJ. Preprint DOI: 10.1101/105437
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Interactions between genetic variation and cellular environment in skeletal muscle gene expression
Taylor DL, Knowles DA, Scott LJ, Ramirez AH, Paolo Casale F, Wolford BN, Guan L, Varshney A, Oliveira Albanus R, Parker SC, 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. Preprint DOI: 10.1101/105429
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The Genetic Architecture of Major Depressive Disorder in Han Chinese Women.
Peterson RE, Cai N, Bigdeli TB, Li Y, Reimers M, Nikulova A, Webb BT, Bacanu SA, Riley BP, Flint J, Kendler KS. JAMA psychiatry Volume 74 (2017) p.162-168 DOI: 10.1001/jamapsychiatry.2016.3578
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Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types.
Ecker S, Chen L, Pancaldi V, Bagger FO, Fernández JM, Carrillo de Santa Pau E, Juan D, Mann AL, Watt S, Casale FP, Sidiropoulos N, Rapin N, Merkel A, BLUEPRINT Consortium, Stunnenberg HG, Stegle O, Frontini M, Downes K, Pastinen T, Kuijpers TW, Rico D, Valencia A, Beck S, Soranzo N, Paul DS. Genome biology Volume 18 (2017) p.18 DOI: 10.1186/s13059-017-1156-8
Genetic Variation in the Social Environment Contributes to Health and Disease.
Baud A, Mulligan MK, Casale FP, Ingels JF, Bohl CJ, Callebert J, Launay JM, Krohn J, Legarra A, Williams RW, Stegle O. PLoS genetics Volume 13 (2017) p.e1006498 DOI: 10.1371/journal.pgen.1006498
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The influence of proton pump inhibitors and other commonly used medication on the gut microbiota.
Imhann F, Vich Vila A, Bonder MJ, Lopez Manosalva AG, Koonen DPY, Fu J, Wijmenga C, Zhernakova A, Weersma RK. Gut microbes Volume 8 (2017) p.351-358 DOI: 10.1080/19490976.2017.1284732
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Molecular and functional variation in iPSC-derived sensory neurons
Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL, Wilbrey A, Bictash M, Impey E, Cao L, Lainez S, Loucif AJ, Whiting PJ, Gutteridge A, Gaffney DJ, HIPSCI Consortium (www.hipsci.org). Preprint DOI: 10.1101/095943
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The emerging landscape of dynamic DNA methylation in early childhood.
Xu CJ, Bonder MJ, Söderhäll C, Bustamante M, Baïz N, Gehring U, Jankipersadsing SA, van der Vlies P, van Diemen CC, van Rijkom B, Just J, Kull I, Kere J, Antó JM, Bousquet J, Zhernakova A, Wijmenga C, Annesi-Maesano I, Sunyer J, Melén E, Li Y, Postma DS, Koppelman GH. BMC genomics Volume 18 (2017) p.25 DOI: 10.1186/s12864-016-3452-1
ODE-Based Modeling of Complex Regulatory Circuits.
Seaton DD. Methods in molecular biology (Clifton, N.J.) Volume 1629 (2017) p.317-330 DOI: 10.1007/978-1-4939-7125-1_20

2016

Genetic variants regulating expression levels and isoform diversity during embryogenesis.
Cannavò E, Koelling N, Harnett D, Garfield D, Casale FP, Ciglar L, Gustafson HE, Viales RR, Marco-Ferreres R, Degner JF, Zhao B, Stegle O, Birney E, Furlong EE. Nature Volume 541 (2017) p.402-406 DOI: 10.1038/nature20802
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Modelling difficulties in abstract thinking in psychosis: the importance of socio-developmental background.
Berg AO, Melle I, Zuber V, Simonsen C, Nerhus M, Ueland T, Andreassen OA, Sundet K, Vaskinn A. Cognitive neuropsychiatry Volume 22 (2017) p.39-52 DOI: 10.1080/13546805.2016.1259998
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Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity.
Wahl S, Drong A, Lehne B, Loh M, Scott WR, Kunze S, Tsai PC, Ried JS, Zhang W, Yang Y, Tan S, Fiorito G, Franke L, Guarrera S, Kasela S, Kriebel J, Richmond RC, Adamo M, Afzal U, Ala-Korpela M, Albetti B, Ammerpohl O, Apperley JF, Beekman M, Bertazzi PA, Black SL, Blancher C, Bonder MJ, Brosch M, Carstensen-Kirberg M, de Craen AJ, de Lusignan S, Dehghan A, Elkalaawy M, Fischer K, Franco OH, Gaunt TR, Hampe J, Hashemi M, Isaacs A, Jenkinson A, Jha S, Kato N, Krogh V, Laffan M, Meisinger C, Meitinger T, Mok ZY, Motta V, Ng HK, Nikolakopoulou Z, Nteliopoulos G, Panico S, Pervjakova N, Prokisch H, Rathmann W, Roden M, Rota F, Rozario MA, Sandling JK, Schafmayer C, Schramm K, Siebert R, Slagboom PE, Soininen P, Stolk L, Strauch K, Tai ES, Tarantini L, Thorand B, Tigchelaar EF, Tumino R, Uitterlinden AG, van Duijn C, van Meurs JB, Vineis P, Wickremasinghe AR, Wijmenga C, Yang TP, Yuan W, Zhernakova A, Batterham RL, Smith GD, Deloukas P, Heijmans BT, Herder C, Hofman A, Lindgren CM, Milani L, van der Harst P, Peters A, Illig T, Relton CL, Waldenberger M, Järvelin MR, Bollati V, Soong R, Spector TD, Scott J, McCarthy MI, Elliott P, Bell JT, Matullo G, Gieger C, Kooner JS, Grallert H, Chambers JC. Nature Volume 541 (2017) p.81-86 DOI: 10.1038/nature20784
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easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies.
Grimm DG, Roqueiro D, Salomé PA, Kleeberger S, Greshake B, Zhu W, Liu C, Lippert C, Stegle O, Schölkopf B, Weigel D, Borgwardt KM. The Plant cell Volume 29 (2017) p.5-19 DOI: 10.1105/tpc.16.00551
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Disease variants alter transcription factor levels and methylation of their binding sites.
Bonder MJ, Luijk R, Zhernakova DV, Moed M, Deelen P, Vermaat M, van Iterson M, van Dijk F, van Galen M, Bot J, Slieker RC, Jhamai PM, Verbiest M, Suchiman HE, Verkerk M, van der Breggen R, van Rooij J, Lakenberg N, Arindrarto W, Kielbasa SM, Jonkers I, van 't Hof P, Nooren I, Beekman M, Deelen J, van Heemst D, Zhernakova A, Tigchelaar EF, Swertz MA, Hofman A, Uitterlinden AG, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, van den Berg LH, van Zwet EW, Mei H, Li Y, Lemire M, Hudson TJ, BIOS Consortium, Slagboom PE, Wijmenga C, Veldink JH, van Greevenbroek MM, van Duijn CM, Boomsma DI, Isaacs A, Jansen R, van Meurs JB, 't Hoen PA, Franke L, Heijmans BT. Nature genetics Volume 49 (2017) p.131-138 DOI: 10.1038/ng.3721
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Identification of context-dependent expression quantitative trait loci in whole blood.
Zhernakova DV, Deelen P, Vermaat M, van Iterson M, van Galen M, Arindrarto W, van 't Hof P, Mei H, van Dijk F, Westra HJ, Bonder MJ, van Rooij J, Verkerk M, Jhamai PM, Moed M, Kielbasa SM, Bot J, Nooren I, Pool R, van Dongen J, Hottenga JJ, Stehouwer CD, van der Kallen CJ, Schalkwijk CG, Zhernakova A, Li Y, Tigchelaar EF, de Klein N, Beekman M, Deelen J, van Heemst D, van den Berg LH, Hofman A, Uitterlinden AG, van Greevenbroek MM, Veldink JH, Boomsma DI, van Duijn CM, Wijmenga C, Slagboom PE, Swertz MA, Isaacs A, van Meurs JB, Jansen R, Heijmans BT, 't Hoen PA, Franke L. Nature genetics Volume 49 (2017) p.139-145 DOI: 10.1038/ng.3737
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Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Cell Volume 167 (2016) p.1897 DOI: 10.1016/j.cell.2016.11.046
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Open Targets: a platform for therapeutic target identification and validation.
Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I. Nucleic acids research Volume 45 (2017) p.D985-D994 DOI: 10.1093/nar/gkw1055
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Scalable latent-factor models applied to single-cell RNA-seq data separate biological drivers from confounding effects
Buettner F, Pratanwanich N, Marioni JC, Stegle O. Preprint DOI: 10.1101/087775
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Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells.
Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Cell Volume 167 (2016) p.1398-1414.e24 DOI: 10.1016/j.cell.2016.10.026
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Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters.
Javierre BM, Burren OS, Wilder SP, Kreuzhuber R, Hill SM, Sewitz S, Cairns J, Wingett SW, Várnai C, Thiecke MJ, Burden F, Farrow S, Cutler AJ, Rehnström K, Downes K, Grassi L, Kostadima M, Freire-Pritchett P, Wang F, BLUEPRINT Consortium, Stunnenberg HG, Todd JA, Zerbino DR, Stegle O, Ouwehand WH, Frontini M, Wallace C, Spivakov M, Fraser P. Cell Volume 167 (2016) p.1369-1384.e19 DOI: 10.1016/j.cell.2016.09.037
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Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.
Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Ter Horst R, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LAB, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ. Cell Volume 167 (2016) p.1125-1136.e8 DOI: 10.1016/j.cell.2016.10.020
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Genome-wide analysis identifies 12 loci influencing human reproductive behavior.
Barban N, Jansen R, de Vlaming R, Vaez A, Mandemakers JJ, Tropf FC, Shen X, Wilson JF, Chasman DI, Nolte IM, Tragante V, van der Laan SW, Perry JR, Kong A, BIOS Consortium, Ahluwalia TS, Albrecht E, Yerges-Armstrong L, Atzmon G, Auro K, Ayers K, Bakshi A, Ben-Avraham D, Berger K, Bergman A, Bertram L, Bielak LF, Bjornsdottir G, Bonder MJ, Broer L, Bui M, Barbieri C, Cavadino A, Chavarro JE, Turman C, Concas MP, Cordell HJ, Davies G, Eibich P, Eriksson N, Esko T, Eriksson J, Falahi F, Felix JF, Fontana MA, Franke L, Gandin I, Gaskins AJ, Gieger C, Gunderson EP, Guo X, Hayward C, He C, Hofer E, Huang H, Joshi PK, Kanoni S, Karlsson R, Kiechl S, Kifley A, Kluttig A, Kraft P, Lagou V, Lecoeur C, Lahti J, Li-Gao R, Lind PA, Liu T, Makalic E, Mamasoula C, Matteson L, Mbarek H, McArdle PF, McMahon G, Meddens SF, Mihailov E, Miller M, Missmer SA, Monnereau C, van der Most PJ, Myhre R, Nalls MA, Nutile T, Kalafati IP, Porcu E, Prokopenko I, Rajan KB, Rich-Edwards J, Rietveld CA, Robino A, Rose LM, Rueedi R, Ryan KA, Saba Y, Schmidt D, Smith JA, Stolk L, Streeten E, Tönjes A, Thorleifsson G, Ulivi S, Wedenoja J, Wellmann J, Willeit P, Yao J, Yengo L, Zhao JH, Zhao W, Zhernakova DV, Amin N, Andrews H, Balkau B, Barzilai N, Bergmann S, Biino G, Bisgaard H, Bønnelykke K, Boomsma DI, Buring JE, Campbell H, Cappellani S, Ciullo M, Cox SR, Cucca F, Toniolo D, Davey-Smith G, Deary IJ, Dedoussis G, Deloukas P, van Duijn CM, de Geus EJ, Eriksson JG, Evans DA, Faul JD, Sala CF, Froguel P, Gasparini P, Girotto G, Grabe HJ, Greiser KH, Groenen PJ, de Haan HG, Haerting J, Harris TB, Heath AC, Heikkilä K, Hofman A, Homuth G, Holliday EG, Hopper J, Hyppönen E, Jacobsson B, Jaddoe VW, Johannesson M, Jugessur A, Kähönen M, Kajantie E, Kardia SL, Keavney B, Kolcic I, Koponen P, Kovacs P, Kronenberg F, Kutalik Z, La Bianca M, Lachance G, Iacono WG, Lai S, Lehtimäki T, Liewald DC, LifeLines Cohort Study, Lindgren CM, Liu Y, Luben R, Lucht M, Luoto R, Magnus P, Magnusson PK, Martin NG, McGue M, McQuillan R, Medland SE, Meisinger C, Mellström D, Metspalu A, Traglia M, Milani L, Mitchell P, Montgomery GW, Mook-Kanamori D, de Mutsert R, Nohr EA, Ohlsson C, Olsen J, Ong KK, Paternoster L, Pattie A, Penninx BW, Perola M, Peyser PA, Pirastu M, Polasek O, Power C, Kaprio J, Raffel LJ, Räikkönen K, Raitakari O, Ridker PM, Ring SM, Roll K, Rudan I, Ruggiero D, Rujescu D, Salomaa V, Schlessinger D, Schmidt H, Schmidt R, Schupf N, Smit J, Sorice R, Spector TD, Starr JM, Stöckl D, Strauch K, Stumvoll M, Swertz MA, Thorsteinsdottir U, Thurik AR, Timpson NJ, Tung JY, Uitterlinden AG, Vaccargiu S, Viikari J, Vitart V, Völzke H, Vollenweider P, Vuckovic D, Waage J, Wagner GG, Wang JJ, Wareham NJ, Weir DR, Willemsen G, Willeit J, Wright AF, Zondervan KT, Stefansson K, Krueger RF, Lee JJ, Benjamin DJ, Cesarini D, Koellinger PD, den Hoed M, Snieder H, Mills MC. Nature genetics Volume 48 (2016) p.1462-1472 DOI: 10.1038/ng.3698
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Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.
Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RWF, Huttenhower C, Dijkstra G, Xavier RJ, Festen EAM, Wijmenga C, Zhernakova A, Weersma RK. Gut Volume 67 (2018) p.108-119 DOI: 10.1136/gutjnl-2016-312135
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The effect of host genetics on the gut microbiome.
Bonder MJ, Kurilshikov A, Tigchelaar EF, Mujagic Z, Imhann F, Vila AV, Deelen P, Vatanen T, Schirmer M, Smeekens SP, Zhernakova DV, Jankipersadsing SA, Jaeger M, Oosting M, Cenit MC, Masclee AA, Swertz MA, Li Y, Kumar V, Joosten L, Harmsen H, Weersma RK, Franke L, Hofker MH, Xavier RJ, Jonkers D, Netea MG, Wijmenga C, Fu J, Zhernakova A. Nature genetics Volume 48 (2016) p.1407-1412 DOI: 10.1038/ng.3663
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Age-related accrual of methylomic variability is linked to fundamental ageing mechanisms.
Slieker RC, van Iterson M, Luijk R, Beekman M, Zhernakova DV, Moed MH, Mei H, van Galen M, Deelen P, Bonder MJ, Zhernakova A, Uitterlinden AG, Tigchelaar EF, Stehouwer CD, Schalkwijk CG, van der Kallen CJ, Hofman A, van Heemst D, de Geus EJ, van Dongen J, Deelen J, van den Berg LH, van Meurs J, Jansen R, 't Hoen PA, Franke L, Wijmenga C, Veldink JH, Swertz MA, van Greevenbroek MM, van Duijn CM, Boomsma DI, BIOS consortium, Slagboom PE, Heijmans BT. Genome biology Volume 17 (2016) p.191 DOI: 10.1186/s13059-016-1053-6
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Warped Matrix Factorisation for Multi-view Data Integration
Pratanwanich N, Lió P, Stegle O. Machine Learning and Knowledge Discovery in Databases. ECML PKDD 2016. Springer , Cham (Lecture Notes in Computer Science, vol 9852) DOI: 10.1007/978-3-319-46227-1_49
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A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.
Lun AT, McCarthy DJ, Marioni JC. F1000Research Volume 5 (2016) p.2122 DOI: 10.12688/f1000research.9501.2
Pleiotropic Analysis of Lung Cancer and Blood Triglycerides.
Zuber V, Marconett CN, Shi J, Hua X, Wheeler W, Yang C, Song L, Dale AM, Laplana M, Risch A, Witoelar A, Thompson WK, Schork AJ, Bettella F, Wang Y, Djurovic S, Zhou B, Borok Z, van der Heijden HF, de Graaf J, Swinkels D, Aben KK, McKay J, Hung RJ, Bikeböller H, Stevens VL, Albanes D, Caporaso NE, Han Y, Wei Y, Panadero MA, Mayordomo JI, Christiani DC, Kiemeney L, Andreassen OA, Houlston R, Amos CI, Chatterjee N, Laird-Offringa IA, Mills IG, Landi MT. Journal of the National Cancer Institute Volume 108 (2016) DOI: 10.1093/jnci/djw167
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A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice.
McIntyre RE, Nicod J, Robles-Espinoza CD, Maciejowski J, Cai N, Hill J, Verstraten R, Iyer V, Rust AG, Balmus G, Mott R, Flint J, Adams DJ. G3 (Bethesda, Md.) Volume 6 (2016) p.2343-2354 DOI: 10.1534/g3.116.030767
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A GWAS meta-analysis suggests roles for xenobiotic metabolism and ion channel activity in the biology of stool frequency.
Jankipersadsing SA, Hadizadeh F, Bonder MJ, Tigchelaar EF, Deelen P, Fu J, Andreasson A, Agreus L, Walter S, Wijmenga C, Hysi P, D'Amato M, Zhernakova A. Gut Volume 66 (2017) p.756-758 DOI: 10.1136/gutjnl-2016-312398
Deep learning for computational biology.
Angermueller C, Pärnamaa T, Parts L, Stegle O. Molecular systems biology Volume 12 (2016) p.878 DOI: 10.15252/msb.20156651
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Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana.
Meng D, Dubin M, Zhang P, Osborne EJ, Stegle O, Clark RM, Nordborg M. PLoS genetics Volume 12 (2016) p.e1006141 DOI: 10.1371/journal.pgen.1006141
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Genome-wide association of multiple complex traits in outbred mice by ultra-low-coverage sequencing.
Nicod J, Davies RW, Cai N, Hassett C, Goodstadt L, Cosgrove C, Yee BK, Lionikaite V, McIntyre RE, Remme CA, Lodder EM, Gregory JS, Hough T, Joynson R, Phelps H, Nell B, Rowe C, Wood J, Walling A, Bopp N, Bhomra A, Hernandez-Pliego P, Callebert J, Aspden RM, Talbot NP, Robbins PA, Harrison M, Fray M, Launay JM, Pinto YM, Blizard DA, Bezzina CR, Adams DJ, Franken P, Weaver T, Wells S, Brown SD, Potter PK, Klenerman P, Lionikas A, Mott R, Flint J. Nature genetics Volume 48 (2016) p.912-918 DOI: 10.1038/ng.3595
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Blood lipids influence DNA methylation in circulating cells.
Dekkers KF, van Iterson M, Slieker RC, Moed MH, Bonder MJ, van Galen M, Mei H, Zhernakova DV, van den Berg LH, Deelen J, van Dongen J, van Heemst D, Hofman A, Hottenga JJ, van der Kallen CJ, Schalkwijk CG, Stehouwer CD, Tigchelaar EF, Uitterlinden AG, Willemsen G, Zhernakova A, Franke L, 't Hoen PA, Jansen R, van Meurs J, Boomsma DI, van Duijn CM, van Greevenbroek MM, Veldink JH, Wijmenga C, BIOS Consortium, van Zwet EW, Slagboom PE, Jukema JW, Heijmans BT. Genome biology Volume 17 (2016) p.138 DOI: 10.1186/s13059-016-1000-6
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GeneCodeq: quality score compression and improved genotyping using a Bayesian framework.
Greenfield DL, Stegle O, Rrustemi A. Bioinformatics (Oxford, England) Volume 32 (2016) p.3124-3132 DOI: 10.1093/bioinformatics/btw385
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Task-Related Edge Density (TED)-A New Method for Revealing Dynamic Network Formation in fMRI Data of the Human Brain.
Lohmann G, Stelzer J, Zuber V, Buschmann T, Margulies D, Bartels A, Scheffler K. PloS one Volume 11 (2016) p.e0158185 DOI: 10.1371/journal.pone.0158185
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Common genetic variation drives molecular heterogeneity in human IPSCs
Kilpinen H, Goncalves A, Leha A, Afzal V, Ashford S, Bala S, Bensaddek D, Casale FP, Culley O, Danacek P, Faulconbridge A, Harrison P, McCarthy D, McCarthy SA, Meleckyte R, Memari Y, Moens N, Soares F, Streeter I, Agu CA, Alderton A, Nelson R, Harper S, Patel M, Clarke L, Halai R, Kirton CM, Kolb-Kokocinski A, Beales P, Birney E, Danovi D, Lamond AI, Ouwehand WH, Vallier L, Watt FM, Durbin R, Stegle O, Gaffney DJ. Preprint DOI: 10.1101/055160
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Population-level analysis of gut microbiome variation.
Falony G, Joossens M, Vieira-Silva S, Wang J, Darzi Y, Faust K, Kurilshikov A, Bonder MJ, Valles-Colomer M, Vandeputte D, Tito RY, Chaffron S, Rymenans L, Verspecht C, De Sutter L, Lima-Mendez G, D'hoe K, Jonckheere K, Homola D, Garcia R, Tigchelaar EF, Eeckhaudt L, Fu J, Henckaerts L, Zhernakova A, Wijmenga C, Raes J. Science (New York, N.Y.) Volume 352 (2016) p.560-564 DOI: 10.1126/science.aad3503
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Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.
Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, LifeLines cohort study, Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J. Science (New York, N.Y.) Volume 352 (2016) p.565-569 DOI: 10.1126/science.aad3369
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CHRONICITY OF DEPRESSION AND MOLECULAR MARKERS IN A LARGE SAMPLE OF HAN CHINESE WOMEN.
Edwards AC, Aggen SH, Cai N, Bigdeli TB, Peterson RE, Docherty AR, Webb BT, Bacanu SA, Flint J, Kendler KS. Depression and anxiety Volume 33 (2016) p.1048-1054 DOI: 10.1002/da.22517
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The influence of a short-term gluten-free diet on the human gut microbiome.
Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, Zhong H, Vatanen T, Gevers D, Wijmenga C, Wang Y, Zhernakova A. Genome medicine Volume 8 (2016) p.45 DOI: 10.1186/s13073-016-0295-y
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Genetic and environmental influences interact with age and sex in shaping the human methylome.
van Dongen J, Nivard MG, Willemsen G, Hottenga JJ, Helmer Q, Dolan CV, Ehli EA, Davies GE, van Iterson M, Breeze CE, Beck S, BIOS Consortium, Suchiman HE, Jansen R, van Meurs JB, Heijmans BT, Slagboom PE, Boomsma DI. Nature communications Volume 7 (2016) p.11115 DOI: 10.1038/ncomms11115
Modelling local gene networks increases power to detect trans-acting genetic effects on gene expression.
Rakitsch B, Stegle O. Genome biology Volume 17 (2016) p.33 DOI: 10.1186/s13059-016-0895-2
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A multiple-phenotype imputation method for genetic studies.
Dahl A, Iotchkova V, Baud A, Johansson Å, Gyllensten U, Soranzo N, Mott R, Kranis A, Marchini J. Nature genetics Volume 48 (2016) p.466-472 DOI: 10.1038/ng.3513
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Refined mapping of autoimmune disease associated genetic variants with gene expression suggests an important role for non-coding RNAs.
Ricaño-Ponce I, Zhernakova DV, Deelen P, Luo O, Li X, Isaacs A, Karjalainen J, Di Tommaso J, Borek ZA, Zorro MM, Gutierrez-Achury J, Uitterlinden AG, Hofman A, van Meurs J, BIOS Consortium, Lifelines Cohort Study, Netea MG, Jonkers IH, Withoff S, van Duijn CM, Li Y, Ruan Y, Franke L, Wijmenga C, Kumar V. Journal of autoimmunity Volume 68 (2016) p.62-74 DOI: 10.1016/j.jaut.2016.01.002
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Classification of low quality cells from single-cell RNA-seq data.
Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ, Marioni JC, Teichmann SA. Genome biology Volume 17 (2016) p.29 DOI: 10.1186/s13059-016-0888-1
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The metabolic background is a global player in Saccharomyces gene expression epistasis.
Alam MT, Zelezniak A, Mülleder M, Shliaha P, Schwarz R, Capuano F, Vowinckel J, Radmanesfahar E, Krüger A, Calvani E, Michel S, Börno S, Christen S, Patil KR, Timmermann B, Lilley KS, Ralser M. Nature microbiology Volume 1 (2016) p.15030 DOI: 10.1038/nmicrobiol.2015.30
ALVIS: interactive non-aggregative visualization and explorative analysis of multiple sequence alignments.
Schwarz RF, Tamuri AU, Kultys M, King J, Godwin J, Florescu AM, Schultz J, Goldman N. Nucleic acids research Volume 44 (2016) p.e77 DOI: 10.1093/nar/gkw022
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Leveraging Genomic Annotations and Pleiotropic Enrichment for Improved Replication Rates in Schizophrenia GWAS.
Wang Y, Thompson WK, Schork AJ, Holland D, Chen CH, Bettella F, Desikan RS, Li W, Witoelar A, Zuber V, Devor A, Bipolar Disorder and Schizophrenia Working Group of the Psychiatric Genomics Consortium, Enhancing Neuro Imaging Genetics through Meta Analysis Consortium, Nöthen MM, Rietschel M, Chen Q, Werge T, Cichon S, Weinberger DR, Djurovic S, O'Donovan M, Visscher PM, Andreassen OA, Dale AM. PLoS genetics Volume 12 (2016) p.e1005803 DOI: 10.1371/journal.pgen.1005803
Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity.
Angermueller C, Clark SJ, Lee HJ, Macaulay IC, Teng MJ, Hu TX, Krueger F, Smallwood S, Ponting CP, Voet T, Kelsey G, Stegle O, Reik W. Nature methods Volume 13 (2016) p.229-232 DOI: 10.1038/nmeth.3728

2015

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An Empirical Bayes Mixture Model for Effect Size Distributions in Genome-Wide Association Studies.
Thompson WK, Wang Y, Schork AJ, Witoelar A, Zuber V, Xu S, Werge T, Holland D, Schizophrenia Working Group of the Psychiatric Genomics Consortium, Andreassen OA, Dale AM. PLoS genetics Volume 11 (2015) p.e1005717 DOI: 10.1371/journal.pgen.1005717
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Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci.
Reppe S, Wang Y, Thompson WK, McEvoy LK, Schork AJ, Zuber V, LeBlanc M, Bettella F, Mills IG, Desikan RS, Djurovic S, Gautvik KM, Dale AM, Andreassen OA, GEFOS Consortium. PloS one Volume 10 (2015) p.e0144531 DOI: 10.1371/journal.pone.0144531
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Timing, rates and spectra of human germline mutation.
Rahbari R, Wuster A, Lindsay SJ, Hardwick RJ, Alexandrov LB, Turki SA, Dominiczak A, Morris A, Porteous D, Smith B, Stratton MR, UK10K Consortium, Hurles ME. Nature genetics Volume 48 (2016) p.126-133 DOI: 10.1038/ng.3469
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destiny: diffusion maps for large-scale single-cell data in R.
Angerer P, Haghverdi L, Büttner M, Theis FJ, Marr C, Buettner F. Bioinformatics (Oxford, England) Volume 32 (2016) p.1241-1243 DOI: 10.1093/bioinformatics/btv715
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Proton pump inhibitors affect the gut microbiome.
Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A. Gut Volume 65 (2016) p.740-748 DOI: 10.1136/gutjnl-2015-310376
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A high-content platform to characterise human induced pluripotent stem cell lines.
Leha A, Moens N, Meleckyte R, Culley OJ, Gervasio MK, Kerz M, Reimer A, Cain SA, Streeter I, Folarin A, Stegle O, Kielty CM, HipSci Consortium, Durbin R, Watt FM, Danovi D. Methods (San Diego, Calif.) Volume 96 (2016) p.85-96 DOI: 10.1016/j.ymeth.2015.11.012
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A Loss-of-Function Variant in a Minor Isoform of ANK3 Protects Against Bipolar Disorder and Schizophrenia.
Hughes T, Hansson L, Sønderby IE, Athanasiu L, Zuber V, Tesli M, Song J, Hultman CM, Bergen SE, Landén M, Melle I, Andreassen OA, Djurovic S. Biological psychiatry Volume 80 (2016) p.323-330 DOI: 10.1016/j.biopsych.2015.09.021
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Genetic Markers of Human Evolution Are Enriched in Schizophrenia.
Srinivasan S, Bettella F, Mattingsdal M, Wang Y, Witoelar A, Schork AJ, Thompson WK, Zuber V, Schizophrenia Working Group of the Psychiatric Genomics Consortium, The International Headache Genetics Consortium, Winsvold BS, Zwart JA, Collier DA, Desikan RS, Melle I, Werge T, Dale AM, Djurovic S, Andreassen OA. Biological psychiatry Volume 80 (2016) p.284-292 DOI: 10.1016/j.biopsych.2015.10.009
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Identifying Novel Gene Variants in Coronary Artery Disease and Shared Genes With Several Cardiovascular Risk Factors.
LeBlanc M, Zuber V, Andreassen BK, Witoelar A, Zeng L, Bettella F, Wang Y, McEvoy LK, Thompson WK, Schork AJ, Reppe S, Barrett-Connor E, Ligthart S, Dehghan A, Gautvik KM, Nelson CP, Schunkert H, Samani NJ, CARDIoGRAM Consortium, Ridker PM, Chasman DI, Aukrust P, Djurovic S, Frigessi A, Desikan RS, Dale AM, Andreassen OA. Circulation research Volume 118 (2016) p.83-94 DOI: 10.1161/circresaha.115.306629
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A global reference for human genetic variation.
1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, Korbel JO, Marchini JL, McCarthy S, McVean GA, Abecasis GR. Nature Volume 526 (2015) p.68-74 DOI: 10.1038/nature15393
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Mondo-Mlx Mediates Organismal Sugar Sensing through the Gli-Similar Transcription Factor Sugarbabe.
Mattila J, Havula E, Suominen E, Teesalu M, Surakka I, Hynynen R, Kilpinen H, Väänänen J, Hovatta I, Käkelä R, Ripatti S, Sandmann T, Hietakangas V. Cell reports Volume 13 (2015) p.350-364 DOI: 10.1016/j.celrep.2015.08.081
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An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, 1000 Genomes Project Consortium, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. Nature Volume 526 (2015) p.75-81 DOI: 10.1038/nature15394
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Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.
Tsang JC, Yu Y, Burke S, Buettner F, Wang C, Kolodziejczyk AA, Teichmann SA, Lu L, Liu P. Genome biology Volume 16 (2015) p.178 DOI: 10.1186/s13059-015-0739-5
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Estimation of Free-Living Energy Expenditure by Heart Rate and Movement Sensing: A Doubly-Labelled Water Study.
Brage S, Westgate K, Franks PW, Stegle O, Wright A, Ekelund U, Wareham NJ. PloS one Volume 10 (2015) p.e0137206 DOI: 10.1371/journal.pone.0137206
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Gain-of-Function Mutations in ZIC1 Are Associated with Coronal Craniosynostosis and Learning Disability.
Twigg SR, Forecki J, Goos JA, Richardson IC, Hoogeboom AJ, van den Ouweland AM, Swagemakers SM, Lequin MH, Van Antwerp D, McGowan SJ, Westbury I, Miller KA, Wall SA, WGS500 Consortium, van der Spek PJ, Mathijssen IM, Pauws E, Merzdorf CS, Wilkie AO. American journal of human genetics Volume 97 (2015) p.378-388 DOI: 10.1016/j.ajhg.2015.07.007
Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C. elegans Locomotion.
Schwarz RF, Branicky R, Grundy LJ, Schafer WR, Brown AE. PLoS computational biology Volume 11 (2015) p.e1004322 DOI: 10.1371/journal.pcbi.1004322
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Population Variation and Genetic Control of Modular Chromatin Architecture in Humans.
Waszak SM, Delaneau O, Gschwind AR, Kilpinen H, Raghav SK, Witwicki RM, Orioli A, Wiederkehr M, Panousis NI, Yurovsky A, Romano-Palumbo L, Planchon A, Bielser D, Padioleau I, Udin G, Thurnheer S, Hacker D, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Cell Volume 162 (2015) p.1039-1050 DOI: 10.1016/j.cell.2015.08.001
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Fine mapping of bone structure and strength QTLs in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, Mont-Cardona C, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T. Bone Volume 81 (2015) p.417-426 DOI: 10.1016/j.bone.2015.08.013
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Gut microbiota composition associated with stool consistency.
Tigchelaar EF, Bonder MJ, Jankipersadsing SA, Fu J, Wijmenga C, Zhernakova A. Gut Volume 65 (2016) p.540-542 DOI: 10.1136/gutjnl-2015-310328
Computational assignment of cell-cycle stage from single-cell transcriptome data.
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F. Methods (San Diego, Calif.) Volume 85 (2015) p.54-61 DOI: 10.1016/j.ymeth.2015.06.021
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Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders.
van Schouwenburg PA, Davenport EE, Kienzler AK, Marwah I, Wright B, Lucas M, Malinauskas T, Martin HC, WGS500 Consortium, Lockstone HE, Cazier JB, Chapel HM, Knight JC, Patel SY. Clinical immunology (Orlando, Fla.) Volume 160 (2015) p.301-314 DOI: 10.1016/j.clim.2015.05.020
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A random forest approach to capture genetic effects in the presence of population structure.
Stephan J, Stegle O, Beyer A. Nature communications Volume 6 (2015) p.7432 DOI: 10.1038/ncomms8432
Efficient set tests for the genetic analysis of correlated traits.
Casale FP, Rakitsch B, Lippert C, Stegle O. Nature methods Volume 12 (2015) p.755-758 DOI: 10.1038/nmeth.3439
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Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations.
Wilson NK, Kent DG, Buettner F, Shehata M, Macaulay IC, Calero-Nieto FJ, Sánchez Castillo M, Oedekoven CA, Diamanti E, Schulte R, Ponting CP, Voet T, Caldas C, Stingl J, Green AR, Theis FJ, Göttgens B. Cell stem cell Volume 16 (2015) p.712-724 DOI: 10.1016/j.stem.2015.04.004
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Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Haghverdi L, Buettner F, Theis FJ. Bioinformatics (Oxford, England) Volume 31 (2015) p.2989-2998 DOI: 10.1093/bioinformatics/btv325
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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. Nature genetics Volume 47 (2015) p.717-726 DOI: 10.1038/ng.3304
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Correction: Abundant Genetic Overlap between Blood Lipids and Immune-Mediated Diseases Indicates Shared Molecular Genetic Mechanisms.
Andreassen OA, Desikan RS, Wang Y, Thompson WK, Schork AJ, Zuber V, Doncheva NT, Ellinghaus E, Albrecht M, Mattingsdal M, Franke A, Lie BA, Mills IG, Aukrust P, McEvoy LK, Djurovic S, Karlsen TH, Dale AM. PloS one Volume 10 (2015) p.e0128048 DOI: 10.1371/journal.pone.0128048
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DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation.
Dubin MJ, Zhang P, Meng D, Remigereau MS, Osborne EJ, Paolo Casale F, Drewe P, Kahles A, Jean G, Vilhjálmsson B, Jagoda J, Irez S, Voronin V, Song Q, Long Q, Rätsch G, Stegle O, Clark RM, Nordborg M. eLife Volume 4 (2015) p.e05255 DOI: 10.7554/elife.05255
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Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.
Rivas MA, Pirinen M, Conrad DF, Lek M, Tsang EK, Karczewski KJ, Karczewski KJ, Maller JB, Kukurba KR, DeLuca DS, Fromer M, Ferreira PG, Smith KS, Zhang R, Zhao F, Banks E, Poplin R, Ruderfer DM, Purcell SM, Tukiainen T, Minikel EV, Stenson PD, Cooper DN, Huang KH, Sullivan TJ, Nedzel J, GTEx Consortium, Geuvadis Consortium, Bustamante CD, Li JB, Daly MJ, Guigo R, Donnelly P, Ardlie K, Sammeth M, Dermitzakis ET, McCarthy MI, Montgomery SB, Lappalainen T, MacArthur DG. Science (New York, N.Y.) Volume 348 (2015) p.666-669 DOI: 10.1126/science.1261877
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A Hybrid of Metabolic Flux Analysis and Bayesian Factor Modeling for Multiomic Temporal Pathway Activation.
Angione C, Pratanwanich N, Lió P. ACS synthetic biology Volume 4 (2015) p.880-889 DOI: 10.1021/sb5003407
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MicroRNAs enrichment in GWAS of complex human phenotypes.
Goulart LF, Bettella F, Sønderby IE, Schork AJ, Thompson WK, Mattingsdal M, Steen VM, Zuber V, Wang Y, Dale AM, PRACTICAL/ELLIPSE consortium, Andreassen OA, Djurovic S. BMC genomics Volume 16 (2015) p.304 DOI: 10.1186/s12864-015-1513-5
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MOZ and BMI1 play opposing roles during Hox gene activation in ES cells and in body segment identity specification in vivo.
Sheikh BN, Downer NL, Phipson B, Vanyai HK, Kueh AJ, McCarthy DJ, Smyth GK, Thomas T, Voss AK. Proceedings of the National Academy of Sciences of the United States of America Volume 112 (2015) p.5437-5442 DOI: 10.1073/pnas.1422872112
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GWAS for executive function and processing speed suggests involvement of the CADM2 gene.
Ibrahim-Verbaas CA, Bressler J, Debette S, Schuur M, Smith AV, Bis JC, Davies G, Trompet S, Smith JA, Wolf C, Chibnik LB, Liu Y, Vitart V, Kirin M, Petrovic K, Polasek O, Zgaga L, Fawns-Ritchie C, Hoffmann P, Karjalainen J, Lahti J, Llewellyn DJ, Schmidt CO, Mather KA, Chouraki V, Sun Q, Resnick SM, Rose LM, Oldmeadow C, Stewart M, Smith BH, Gudnason V, Yang Q, Mirza SS, Jukema JW, deJager PL, Harris TB, Liewald DC, Amin N, Coker LH, Stegle O, Lopez OL, Schmidt R, Teumer A, Ford I, Karbalai N, Becker JT, Jonsdottir MK, Au R, Fehrmann R, Herms S, Nalls M, Zhao W, Turner ST, Yaffe K, Lohman K, van Swieten JC, Kardia S, Knopman DS, Meeks WM, Heiss G, Holliday EG, Schofield PW, Tanaka T, Stott DJ, Wang J, Ridker P, Gow AJ, Pattie A, Starr JM, Hocking LJ, Armstrong NJ, McLachlan S, Shulman JM, Pilling LC, Eiriksdottir G, Scott RJ, Kochan NA, Palotie A, Hsieh YC, Eriksson JG, Penman A, Gottesman RF, Oostra BA, Yu L, DeStefano AL, Beiser A, Garcia M, Rotter JI, Nöthen MM, Hofman A, Slagboom PE, Westendorp R, Buckley BM, Wolf PA, Uitterlinden AG, Psaty BM, Grabe HJ, Bandinelli S, Chasman DI, Grodstein F, Räikkönen K, Lambert JC, Porteous DJ, Generation Scotland, Price JF, Sachdev PS, Ferrucci L, Attia JR, Rudan I, Hayward C, Wright AF, Wilson JF, Cichon S, Franke L, Schmidt H, Ding J, de Craen A, Fornage M, Bennett DA, Deary IJ, Ikram MA, Launer LJ, Fitzpatrick AL, Seshadri S, van Duijn CM, Mosley TH. Molecular psychiatry Volume 21 (2016) p.189-197 DOI: 10.1038/mp.2015.37
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Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms.
Andreassen OA, Desikan RS, Wang Y, Thompson WK, Schork AJ, Zuber V, Doncheva NT, Ellinghaus E, Albrecht M, Mattingsdal M, Franke A, Lie BA, Mills IG, Aukrust P, McEvoy LK, Djurovic S, Karlsen TH, Dale AM. PloS one Volume 10 (2015) p.e0123057 DOI: 10.1371/journal.pone.0123057
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Effects of high-dose oral insulin on immune responses in children at high risk for type 1 diabetes: the Pre-POINT randomized clinical trial.
Bonifacio E, Ziegler AG, Klingensmith G, Schober E, Bingley PJ, Rottenkolber M, Theil A, Eugster A, Puff R, Peplow C, Buettner F, Lange K, Hasford J, Achenbach P, Pre-POINT Study Group. JAMA Volume 313 (2015) p.1541-1549 DOI: 10.1001/jama.2015.2928
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Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.
Schwarz RF, Ng CK, Cooke SL, Newman S, Temple J, Piskorz AM, Gale D, Sayal K, Murtaza M, Baldwin PJ, Rosenfeld N, Earl HM, Sala E, Jimenez-Linan M, Parkinson CA, Markowetz F, Brenton JD. PLoS medicine Volume 12 (2015) p.e1001789 DOI: 10.1371/journal.pmed.1001789
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Decoding the regulatory network of early blood development from single-cell gene expression measurements.
Moignard V, Woodhouse S, Haghverdi L, Lilly AJ, Tanaka Y, Wilkinson AC, Buettner F, Macaulay IC, Jawaid W, Diamanti E, Nishikawa SI, Piterman N, Kouskoff V, Theis FJ, Fisher J, Göttgens B. Nature biotechnology Volume 33 (2015) p.269-276 DOI: 10.1038/nbt.3154
Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC. Nature reviews. Genetics Volume 16 (2015) p.133-145 DOI: 10.1038/nrg3833
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A, Theis FJ, Teichmann SA, Marioni JC, Stegle O. Nature biotechnology Volume 33 (2015) p.155-160 DOI: 10.1038/nbt.3102
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Century-scale methylome stability in a recently diverged Arabidopsis thaliana lineage.
Hagmann J, Becker C, Müller J, Stegle O, Meyer RC, Wang G, Schneeberger K, Fitz J, Altmann T, Bergelson J, Borgwardt K, Weigel D. PLoS genetics Volume 11 (2015) p.e1004920 DOI: 10.1371/journal.pgen.1004920
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Erratum to: Feature ranking of type 1 diabetes susceptibility genes improves prediction of type 1 diabetes.
Winkler C, Krumsiek J, Buettner F, Angermüller C, Giannopoulou EZ, Theis FJ, Ziegler AG, Bonifacio E. Diabetologia Volume 58 (2015) p.206 DOI: 10.1007/s00125-014-3435-1
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Personalized medicine: from genotypes, molecular phenotypes and the quantified self, towards improved medicine.
Dudley JT, Listgarten J, Stegle O, Brenner SE, Parts L. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2015) p.342-346
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Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.
Lehmann KV, Kahles A, Kandoth C, Lee W, Schultz N, Stegle O, Rätsch G. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2015) p.44-55

2014

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Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis.
Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I, Loudet O. The Plant cell Volume 26 (2014) p.4298-4310 DOI: 10.1105/tpc.114.130310
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Genome-wide studies of verbal declarative memory in nondemented older people: the Cohorts for Heart and Aging Research in Genomic Epidemiology consortium.
Debette S, Ibrahim Verbaas CA, Bressler J, Schuur M, Smith A, Bis JC, Davies G, Wolf C, Gudnason V, Chibnik LB, Yang Q, deStefano AL, de Quervain DJ, Srikanth V, Lahti J, Grabe HJ, Smith JA, Priebe L, Yu L, Karbalai N, Hayward C, Wilson JF, Campbell H, Petrovic K, Fornage M, Chauhan G, Yeo R, Boxall R, Becker J, Stegle O, Mather KA, Chouraki V, Sun Q, Rose LM, Resnick S, Oldmeadow C, Kirin M, Wright AF, Jonsdottir MK, Au R, Becker A, Amin N, Nalls MA, Turner ST, Kardia SL, Oostra B, Windham G, Coker LH, Zhao W, Knopman DS, Heiss G, Griswold ME, Gottesman RF, Vitart V, Hastie ND, Zgaga L, Rudan I, Polasek O, Holliday EG, Schofield P, Schofield P, Choi SH, Tanaka T, An Y, Perry RT, Kennedy RE, Sale MM, Wang J, Wadley VG, Liewald DC, Ridker PM, Gow AJ, Pattie A, Starr JM, Porteous D, Liu X, Thomson R, Armstrong NJ, Eiriksdottir G, Assareh AA, Kochan NA, Widen E, Palotie A, Hsieh YC, Eriksson JG, Vogler C, van Swieten JC, Shulman JM, Beiser A, Rotter J, Schmidt CO, Hoffmann W, Nöthen MM, Ferrucci L, Attia J, Uitterlinden AG, Amouyel P, Dartigues JF, Amieva H, Räikkönen K, Garcia M, Wolf PA, Hofman A, Longstreth WT, Psaty BM, Boerwinkle E, DeJager PL, Sachdev PS, Schmidt R, Breteler MM, Teumer A, Lopez OL, Cichon S, Chasman DI, Grodstein F, Müller-Myhsok B, Tzourio C, Papassotiropoulos A, Bennett DA, Ikram MA, Deary IJ, van Duijn CM, Launer L, Fitzpatrick AL, Seshadri S, Mosley TH, Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium. Biological psychiatry Volume 77 (2015) p.749-763 DOI: 10.1016/j.biopsych.2014.08.027
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Synaptic, transcriptional and chromatin genes disrupted in autism.
De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, Kou Y, Liu L, Fromer M, Walker S, Singh T, Klei L, Kosmicki J, Shih-Chen F, Aleksic B, Biscaldi M, Bolton PF, Brownfeld JM, Cai J, Campbell NG, Carracedo A, Chahrour MH, Chiocchetti AG, Coon H, Crawford EL, Curran SR, Dawson G, Duketis E, Fernandez BA, Gallagher L, Geller E, Guter SJ, Hill RS, Ionita-Laza J, Jimenz Gonzalez P, Kilpinen H, Klauck SM, Kolevzon A, Lee I, Lei I, Lei J, Lehtimäki T, Lin CF, Ma'ayan A, Marshall CR, McInnes AL, Neale B, Owen MJ, Ozaki N, Parellada M, Parr JR, Purcell S, Puura K, Rajagopalan D, Rehnström K, Reichenberg A, Sabo A, Sachse M, Sanders SJ, Schafer C, Schulte-Rüther M, Skuse D, Stevens C, Szatmari P, Tammimies K, Valladares O, Voran A, Li-San W, Weiss LA, Willsey AJ, Yu TW, Yuen RK, DDD Study, Homozygosity Mapping Collaborative for Autism, UK10K Consortium, Cook EH, Freitag CM, Gill M, Hultman CM, Lehner T, Palotie A, Schellenberg GD, Sklar P, State MW, Sutcliffe JS, Walsh CA, Scherer SW, Zwick ME, Barett JC, Cutler DJ, Roeder K, Devlin B, Daly MJ, Buxbaum JD. Nature Volume 515 (2014) p.209-215 DOI: 10.1038/nature13772
Cancer evolution: mathematical models and computational inference.
Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F. Systematic biology Volume 64 (2015) p.e1-25 DOI: 10.1093/sysbio/syu081
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Warped linear mixed models for the genetic analysis of transformed phenotypes.
Fusi N, Lippert C, Lawrence ND, Stegle O. Nature communications Volume 5 (2014) p.4890 DOI: 10.1038/ncomms5890
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RAMONA: a Web application for gene set analysis on multilevel omics data.
Sass S, Buettner F, Mueller NS, Theis FJ. Bioinformatics (Oxford, England) Volume 31 (2015) p.128-130 DOI: 10.1093/bioinformatics/btu610
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Sequence Bundles: a novel method for visualising, discovering and exploring sequence motifs.
Kultys M, Nicholas L, Schwarz R, Goldman N, King J. BMC proceedings Volume 8 (2014) p.S8 DOI: 10.1186/1753-6561-8-s2-s8
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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium. Nature biotechnology Volume 32 (2014) p.903-914 DOI: 10.1038/nbt.2957
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Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, Andrews SR, Stegle O, Reik W, Kelsey G. Nature methods Volume 11 (2014) p.817-820 DOI: 10.1038/nmeth.3035
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High-resolution genome screen for bone mineral density in heterogeneous stock rat.
Alam I, Koller DL, Cañete T, Blázquez G, López-Aumatell R, Martínez-Membrives E, Díaz-Morán S, Tobeña A, Fernández-Teruel A, Stridh P, Diez M, Olsson T, Johannesson M, Baud A, Econs MJ, Foroud T. Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research Volume 29 (2014) p.1619-1626 DOI: 10.1002/jbmr.2195
Genomes and phenomes of a population of outbred rats and its progenitors.
Baud A, Guryev V, Hummel O, Johannesson M, Rat Genome Sequencing and Mapping Consortium, Flint J. Scientific data Volume 1 (2014) p.140011 DOI: 10.1038/sdata.2014.11
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Transparent thin shield for radio frequency transmit coils.
Rivera DS, Schulz J, Siegert T, Zuber V, Turner R. Magma (New York, N.Y.) Volume 28 (2015) p.49-56 DOI: 10.1007/s10334-014-0448-1
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LIMIX: genetic analysis of multiple traits
Lippert C, Casale FP, Rakitsch B, Stegle O. Preprint DOI: 10.1101/003905
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Protease inhibitor 15, a candidate gene for abdominal aortic internal elastic lamina ruptures in the rat.
Falak S, Schafer S, Baud A, Hummel O, Schulz H, Gauguier D, Hubner N, Osborne-Pellegrin M. Physiological genomics Volume 46 (2014) p.418-428 DOI: 10.1152/physiolgenomics.00004.2014
Phylogenetic quantification of intra-tumour heterogeneity.
Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F. PLoS computational biology Volume 10 (2014) p.e1003535 DOI: 10.1371/journal.pcbi.1003535
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Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat.
Tuncel J, Haag S, Yau AC, Norin U, Baud A, Lönnblom E, Maratou K, Ytterberg AJ, Ekman D, Thordardottir S, Johannesson M, Gillett A, EURATRANS Consortium, Stridh P, Jagodic M, Olsson T, Fernández-Teruel A, Zubarev RA, Mott R, Aitman TJ, Flint J, Holmdahl R. PLoS genetics Volume 10 (2014) p.e1004151 DOI: 10.1371/journal.pgen.1004151
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Genetic pleiotropy between multiple sclerosis and schizophrenia but not bipolar disorder: differential involvement of immune-related gene loci.
Andreassen OA, Harbo HF, Wang Y, Thompson WK, Schork AJ, Mattingsdal M, Zuber V, Bettella F, Ripke S, Kelsoe JR, Kendler KS, O'Donovan MC, Sklar P, Psychiatric Genomics Consortium (PGC) Bipolar Disorder and Schizophrenia Work Groups, International Multiple Sclerosis Genetics Consortium (IMSGC), McEvoy LK, Desikan RS, Lie BA, Djurovic S, Dale AM. Molecular psychiatry Volume 20 (2015) p.207-214 DOI: 10.1038/mp.2013.195
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The architecture of parent-of-origin effects in mice.
Mott R, Yuan W, Kaisaki P, Gan X, Cleak J, Edwards A, Baud A, Flint J. Cell Volume 156 (2014) p.332-342 DOI: 10.1016/j.cell.2013.11.043

2013

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Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
Waszak SM, Kilpinen H, Gschwind AR, Orioli A, Raghav SK, Witwicki RM, Migliavacca E, Yurovsky A, Lappalainen T, Hernandez N, Reymond A, Dermitzakis ET, Deplancke B. Bioinformatics (Oxford, England) Volume 30 (2014) p.165-171 DOI: 10.1093/bioinformatics/btt667
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Allele-specific regulation of DISC1 expression by miR-135b-5p.
Rossi M, Kilpinen H, Muona M, Surakka I, Ingle C, Lahtinen J, Hennah W, Ripatti S, Hovatta I. European journal of human genetics : EJHG Volume 22 (2014) p.840-843 DOI: 10.1038/ejhg.2013.246
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Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription.
Kilpinen H, Waszak SM, Gschwind AR, Raghav SK, Witwicki RM, Orioli A, Migliavacca E, Wiederkehr M, Gutierrez-Arcelus M, Panousis NI, Yurovsky A, Lappalainen T, Romano-Palumbo L, Planchon A, Bielser D, Bryois J, Padioleau I, Udin G, Thurnheer S, Hacker D, Core LJ, Lis JT, Hernandez N, Reymond A, Deplancke B, Dermitzakis ET. Science (New York, N.Y.) Volume 342 (2013) p.744-747 DOI: 10.1126/science.1242463
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Genotype-environment interactions reveal causal pathways that mediate genetic effects on phenotype.
Gagneur J, Stegle O, Zhu C, Jakob P, Tekkedil MM, Aiyar RS, Schuon AK, Pe'er D, Steinmetz LM. PLoS genetics Volume 9 (2013) p.e1003803 DOI: 10.1371/journal.pgen.1003803
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Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG, Barann M, Wieland T, Greger L, van Iterson M, Almlöf J, Ribeca P, Pulyakhina I, Esser D, Giger T, Tikhonov A, Sultan M, Bertier G, MacArthur DG, Lek M, Lizano E, Buermans HP, Padioleau I, Schwarzmayr T, Karlberg O, Ongen H, Kilpinen H, Beltran S, Gut M, Kahlem K, Amstislavskiy V, Stegle O, Pirinen M, Montgomery SB, Donnelly P, McCarthy MI, Flicek P, Strom TM, Geuvadis Consortium, Lehrach H, Schreiber S, Sudbrak R, Carracedo A, Antonarakis SE, Häsler R, Syvänen AC, van Ommen GJ, Brazma A, Meitinger T, Rosenstiel P, Guigó R, Gut IG, Estivill X, Dermitzakis ET. Nature Volume 501 (2013) p.506-511 DOI: 10.1038/nature12531
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Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, Pulyakhina I, Anvar SY, Laros JF, Buermans HP, Karlberg O, Brännvall M, GEUVADIS Consortium, den Dunnen JT, van Ommen GJ, Gut IG, Guigó R, Estivill X, Syvänen AC, Dermitzakis ET, Lappalainen T. Nature biotechnology Volume 31 (2013) p.1015-1022 DOI: 10.1038/nbt.2702
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[Genome sequencing and genetic mapping to dissect the genetic basis of complex traits].
Baud A, Calderari S, Mott R, Flint J, Gauguier D, Rat Genome Sequencing and Mapping Consortium. Medecine sciences : M/S Volume 29 (2013) p.671-674 DOI: 10.1051/medsci/2013296024
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Accurate detection of differential RNA processing.
Drewe P, Stegle O, Hartmann L, Kahles A, Bohnert R, Wachter A, Borgwardt K, Rätsch G. Nucleic acids research Volume 41 (2013) p.5189-5198 DOI: 10.1093/nar/gkt211
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Detecting regulatory gene-environment interactions with unmeasured environmental factors.
Fusi N, Lippert C, Borgwardt K, Lawrence ND, Stegle O. Bioinformatics (Oxford, England) Volume 29 (2013) p.1382-1389 DOI: 10.1093/bioinformatics/btt148
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A Palaeolithic-type diet causes strong tissue-specific effects on ectopic fat deposition in obese postmenopausal women.
Ryberg M, Sandberg S, Mellberg C, Stegle O, Lindahl B, Larsson C, Hauksson J, Olsson T. Journal of internal medicine Volume 274 (2013) p.67-76 DOI: 10.1111/joim.12048
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The future of genome-based medicine.
Morris Q, Brenner SE, Listgarten J, Stegle O. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2013) p.456-458
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PERSONALIZED MEDICINE: FROM GENOTYPES AND MOLECULAR PHENOTYPES TOWARDS COMPUTED THERAPY.
Stegle O, Brenner SE, Morris Q, Listgarten J. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Volume 18 (2013) p.171-174

2012

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A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K. Bioinformatics (Oxford, England) Volume 29 (2013) p.206-214 DOI: 10.1093/bioinformatics/bts669
*
Common variant at 16p11.2 conferring risk of psychosis.
Steinberg S, de Jong S, Mattheisen M, Costas J, Demontis D, Jamain S, Pietiläinen OP, Lin K, Papiol S, Huttenlocher J, Sigurdsson E, Vassos E, Giegling I, Breuer R, Fraser G, Walker N, Melle I, Djurovic S, Agartz I, Tuulio-Henriksson A, Suvisaari J, Lönnqvist J, Paunio T, Olsen L, Hansen T, Ingason A, Pirinen M, Strengman E, GROUP, Hougaard DM, Orntoft T, Didriksen M, Hollegaard MV, Nordentoft M, Abramova L, Kaleda V, Arrojo M, Sanjuán J, Arango C, Etain B, Bellivier F, Méary A, Schürhoff F, Szoke A, Ribolsi M, Magni V, Siracusano A, Sperling S, Rossner M, Christiansen C, Kiemeney LA, Franke B, van den Berg LH, Veldink J, Curran S, Bolton P, Poot M, Staal W, Rehnstrom K, Kilpinen H, Freitag CM, Meyer J, Magnusson P, Saemundsen E, Martsenkovsky I, Bikshaieva I, Martsenkovska I, Vashchenko O, Raleva M, Paketchieva K, Stefanovski B, Durmishi N, Pejovic Milovancevic M, Lecic Tosevski D, Silagadze T, Naneishvili N, Mikeladze N, Surguladze S, Vincent JB, Farmer A, Mitchell PB, Wright A, Schofield PR, Fullerton JM, Montgomery GW, Martin NG, Rubino IA, van Winkel R, Kenis G, De Hert M, Réthelyi JM, Bitter I, Terenius L, Jönsson EG, Bakker S, van Os J, Jablensky A, Leboyer M, Bramon E, Powell J, Murray R, Corvin A, Gill M, Morris D, O'Neill FA, Kendler K, Riley B, Wellcome Trust Case Control Consortium 2, Craddock N, Owen MJ, O'Donovan MC, Thorsteinsdottir U, Kong A, Ehrenreich H, Carracedo A, Golimbet V, Andreassen OA, Børglum AD, Mors O, Mortensen PB, Werge T, Ophoff RA, Nöthen MM, Rietschel M, Cichon S, Ruggeri M, Tosato S, Palotie A, St Clair D, Rujescu D, Collier DA, Stefansson H, Stefansson K. Molecular psychiatry Volume 19 (2014) p.108-114 DOI: 10.1038/mp.2012.157
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How next-generation sequencing is transforming complex disease genetics.
Kilpinen H, Barrett JC. Trends in genetics : TIG Volume 29 (2013) p.23-30 DOI: 10.1016/j.tig.2012.10.001
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Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.
Yuan Y, Failmezger H, Rueda OM, Ali HR, Gräf S, Chin SF, Schwarz RF, Curtis C, Dunning MJ, Bardwell H, Johnson N, Doyle S, Turashvili G, Provenzano E, Aparicio S, Caldas C, Markowetz F. Science translational medicine Volume 4 (2012) p.157ra143 DOI: 10.1126/scitranslmed.3004330
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Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.
Windram O, Madhou P, McHattie S, Hill C, Hickman R, Cooke E, Jenkins DJ, Penfold CA, Baxter L, Breeze E, Kiddle SJ, Rhodes J, Atwell S, Kliebenstein DJ, Kim YS, Stegle O, Borgwardt K, Zhang C, Tabrett A, Legaie R, Moore J, Finkenstadt B, Wild DL, Mead A, Rand D, Beynon J, Ott S, Buchanan-Wollaston V, Denby KJ. The Plant cell Volume 24 (2012) p.3530-3557 DOI: 10.1105/tpc.112.102046
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Diverse epigenetic strategies interact to control epidermal differentiation.
Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, Sirokmány G, Donati G, Uribe-Lewis S, Pavlidis P, Murrell A, Markowetz F, Watt FM. Nature cell biology Volume 14 (2012) p.753-763 DOI: 10.1038/ncb2520
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Patterns of cis regulatory variation in diverse human populations.
Stranger BE, Montgomery SB, Dimas AS, Parts L, Stegle O, Ingle CE, Sekowska M, Smith GD, Evans D, Gutierrez-Arcelus M, Price A, Raj T, Nisbett J, Nica AC, Beazley C, Durbin R, Deloukas P, Dermitzakis ET. PLoS genetics Volume 8 (2012) p.e1002639 DOI: 10.1371/journal.pgen.1002639
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Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses.
Stegle O, Parts L, Piipari M, Winn J, Durbin R. Nature protocols Volume 7 (2012) p.500-507 DOI: 10.1038/nprot.2011.457
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ShapePheno: unsupervised extraction of shape phenotypes from biological image collections.
Karaletsos T, Stegle O, Dreyer C, Winn J, Borgwardt KM. Bioinformatics (Oxford, England) Volume 28 (2012) p.1001-1008 DOI: 10.1093/bioinformatics/bts081
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Joint modelling of confounding factors and prominent genetic regulators provides increased accuracy in genetical genomics studies.
Fusi N, Stegle O, Lawrence ND. PLoS computational biology Volume 8 (2012) p.e1002330 DOI: 10.1371/journal.pcbi.1002330