Publications

Publications

2017

Impact of Alternative Splicing on the Human Proteome.
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO.
Cell reports Volume 20 (2017) p.1229-1241

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.
Lun ATL, Marioni JC.
Biostatistics (Oxford, England) Volume 18 (2017) p.451-464

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.
Huang Y, Kim JK, Do DV, Lee C, Penfold CA, Zylicz JJ, Marioni JC, Hackett JA, Surani MA.
eLife Volume 6 (2017) p.

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.
Mohammed H, Hernando-Herraez I, Savino A, Scialdone A, Macaulay I, Mulas C, Chandra T, Voet T, Dean W, Nichols J, Marioni JC, Reik W.
Cell reports Volume 20 (2017) p.1215-1228

Normalizing single-cell RNA sequencing data: challenges and opportunities.
Vallejos CA, Risso D, Scialdone A, Dudoit S, Marioni JC.
Nature methods Volume 14 (2017) p.565-571

Testing for differential abundance in mass cytometry data.
Lun ATL, Richard AC, Marioni JC.
Nature methods Volume 14 (2017) p.707-709

Aging increases cell-to-cell transcriptional variability upon immune stimulation.
Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT.
Science (New York, N.Y.) Volume 355 (2017) p.1433-1436

2016

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.
Rudolph KL, Schmitt BM, Villar D, White RJ, Marioni JC, Kutter C, Odom DT.
PLoS genetics Volume 12 (2016) p.e1006024

Resolving early mesoderm diversification through single-cell expression profiling.
Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC, Göttgens B.
Nature Volume 535 (2016) p.289-293

Structure and evolutionary history of a large family of NLR proteins in the zebrafish.
Howe K, Schiffer PH, Zielinski J, Wiehe T, Laird GK, Marioni JC, Soylemez O, Kondrashov F, Leptin M.
Open biology Volume 6 (2016) p.160009

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.
Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M.
Cell Volume 165 (2016) p.61-74

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

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

Beyond comparisons of means: understanding changes in gene expression at the single-cell level.
Vallejos CA, Richardson S, Marioni JC.
Genome biology Volume 17 (2016) p.70

Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.
Ernst C, Pike J, Aitken SJ, Long HK, Eling N, Stojic L, Ward MC, Connor F, Rayner TF, Lukk M, Klose RJ, Kutter C, Odom DT.
eLife Volume 5 (2016) p.

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Lun AT, Bach K, Marioni JC.
Genome biology Volume 17 (2016) p.75

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC.
Nature communications Volume 7 (2016) p.10415

HDTD: analyzing multi-tissue gene expression data.
Touloumis A, Marioni JC, Tavaré S.
Bioinformatics (Oxford, England) Volume 32 (2016) p.2193-2195

Sirtuin 1 stimulates the proliferation and the expression of glycolysis genes in pancreatic neoplastic lesions.
Pinho AV, Mawson A, Gill A, Arshi M, Warmerdam M, Giry-Laterriere M, Eling N, Lie T, Kuster E, Camargo S, Biankin AV, Wu J, Rooman I.
Oncotarget Volume 7 (2016) p.74768-74778

2015

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.
Leigh-Brown S, Goncalves A, Thybert D, Stefflova K, Watt S, Flicek P, Brazma A, Marioni JC, Odom DT.
PloS one Volume 10 (2015) p.e0137367

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC.
Nature communications Volume 6 (2015) p.8687

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.
Saraiva LR, Ibarra-Soria X, Khan M, Omura M, Scialdone A, Mombaerts P, Marioni JC, Logan DW.
Scientific reports Volume 5 (2015) p.18178

Testing the mean matrix in high-dimensional transposable data.
Touloumis A, Tavaré S, Marioni JC.
Biometrics Volume 71 (2015) p.157-166

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

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA.
Cell stem cell Volume 17 (2015) p.471-485

Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC.
Nature reviews. Genetics Volume 16 (2015) p.133-145

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR.
Genome biology Volume 16 (2015) p.201

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.
Saraiva LR, Ahuja G, Ivandic I, Syed AS, Marioni JC, Korsching SI, Logan DW.
Scientific reports Volume 5 (2015) p.11487

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.
Achim K, Pettit JB, Saraiva LR, Gavriouchkina D, Larsson T, Arendt D, Marioni JC.
Nature biotechnology Volume 33 (2015) p.503-509

The technology and biology of single-cell RNA sequencing.
Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA.
Molecular cell Volume 58 (2015) p.610-620

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

Emerging Drug Target In Pancreatic Cancer: Placing Sirtuin 1 on the Canvas.
Giry-Laterriere M, Pinho AV, Eling N, Chantrill L, Rooman I.
Current cancer drug targets Volume 15 (2015) p.463-468

Identification of artesunate as a specific activator of ferroptosis in pancreatic cancer cells.
Eling N, Reuter L, Hazin J, Hamacher-Brady A, Brady NR.
Oncoscience Volume 2 (2015) p.517-532

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Vallejos CA, Marioni JC, Richardson S.
PLoS computational biology Volume 11 (2015) p.e1004333

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone.
Piccirillo SG, Spiteri I, Sottoriva A, Touloumis A, Ber S, Price SJ, Heywood R, Francis NJ, Howarth KD, Collins VP, Venkitaraman AR, Curtis C, Marioni JC, Tavaré S, Watts C.
Cancer research Volume 75 (2015) p.194-202

2014

Random monoallelic gene expression increases upon embryonic stem cell differentiation.
Eckersley-Maslin MA, Thybert D, Bergmann JH, Marioni JC, Flicek P, Spector DL.
Developmental cell Volume 28 (2014) p.351-365

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments.
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, Huber W, Jupp S, Keays M, Kryvych N, McMurry J, Marioni JC, Malone J, Megy K, Rustici G, Tang AY, Taubert J, Williams E, Mannion O, Parkinson HE, Brazma A.
Nucleic acids research Volume 42 (2014) p.D926-32

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.
Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F.
Nature genetics Volume 46 (2014) p.753-758

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.
Peat JR, Dean W, Clark SJ, Krueger F, Smallwood SA, Ficz G, Kim JK, Marioni JC, Hore TA, Reik W.
Cell reports Volume 9 (2014) p.1990-2000

Identifying cell types from spatially referenced single-cell expression datasets.
Pettit JB, Tomer R, Achim K, Richardson S, Azizi L, Marioni J.
PLoS computational biology Volume 10 (2014) p.e1003824

Single Cell Genomics meeting in Stockholm: from single cells to cell types.
Scialdone A, Achim K, Marioni JC.
Genome biology Volume 15 (2014) p.496

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways.
Ballester B, Medina-Rivera A, Schmidt D, Gonzàlez-Porta M, Carlucci M, Chen X, Chessman K, Faure AJ, Funnell AP, Goncalves A, Kutter C, Lukk M, Menon S, McLaren WM, Stefflova K, Watt S, Weirauch MT, Crossley M, Marioni JC, Odom DT, Flicek P, Wilson MD.
eLife Volume 3 (2014) p.e02626

RNA-Seq gene profiling--a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A.
PloS one Volume 9 (2014) p.e107026

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface.
Schmitt BM, Rudolph KL, Karagianni P, Fonseca NA, White RJ, Talianidis I, Odom DT, Marioni JC, Kutter C.
Genome research Volume 24 (2014) p.1797-1807

2013

Accounting for technical noise in single-cell RNA-seq experiments.
Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG.
Nature methods Volume 10 (2013) p.1093-1095

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim JK, Marioni JC.
Genome biology Volume 14 (2013) p.R7

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.
Sottoriva A, Spiteri I, Piccirillo SG, Touloumis A, Collins VP, Marioni JC, Curtis C, Watts C, Tavaré S.
Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.4009-4014

bioWeb3D: an online webGL 3D data visualisation tool.
Pettit JB, Marioni JC.
BMC bioinformatics Volume 14 (2013) p.185

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals.
Stefflova K, Thybert D, Wilson MD, Streeter I, Aleksic J, Karagianni P, Brazma A, Adams DJ, Talianidis I, Marioni JC, Flicek P, Odom DT.
Cell Volume 154 (2013) p.530-540

Peroxiredoxin-3 is overexpressed in prostate cancer and promotes cancer cell survival by protecting cells from oxidative stress.
Whitaker HC, Patel D, Howat WJ, Warren AY, Kay JD, Sangan T, Marioni JC, Mitchell J, Aldridge S, Luxton HJ, Massie C, Lynch AG, Neal DE.
British journal of cancer Volume 109 (2013) p.983-993

2012

Comparative RNA sequencing reveals substantial genetic variation in endangered primates.
Perry GH, Melsted P, Marioni JC, Wang Y, Bainer R, Pickrell JK, Michelini K, Zehr S, Yoder AD, Stephens M, Pritchard JK, Gilad Y.
Genome research Volume 22 (2012) p.602-610

Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC.
Bioinformatics (Oxford, England) Volume 28 (2012) p.3169-3177

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.
Goncalves A, Leigh-Brown S, Thybert D, Stefflova K, Turro E, Flicek P, Brazma A, Odom DT, Marioni JC.
Genome research Volume 22 (2012) p.2376-2384

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.
Barreiro LB, Tailleux L, Pai AA, Gicquel B, Marioni JC, Gilad Y.
Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.1204-1209

2011

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.
Pai AA, Bell JT, Marioni JC, Pritchard JK, Gilad Y.
PLoS Genetics Volume 7 (2011) p.e1001316

Integrative analysis of array-comparative genomic hybridisation and matched gene expression profiling data reveals novel genes with prognostic significance in oesophageal adenocarcinoma.
Goh XY, Rees JR, Paterson AL, Chin SF, Marioni JC, Save V, O'Donovan M, Eijk PP, Alderson D, Ylstra B, Caldas C, Fitzgerald RC.
Gut Volume 60 (2011) p.1317-1326

The variant call format and VCFtools.
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group.
Bioinformatics (Oxford, England) Volume 27 (2011) p.2156-2158

Gene expression differences among primates are associated with changes in a histone epigenetic modification.
Cain CE, Blekhman R, Marioni JC, Gilad Y.
Genetics Volume 187 (2011) p.1225-1234

2010

Understanding mechanisms underlying human gene expression variation with RNA sequencing.
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK.
Nature Volume 464 (2010) p.768-772

Sex-specific and lineage-specific alternative splicing in primates.
Blekhman R, Marioni JC, Zumbo P, Stephens M, Gilad Y.
Genome research Volume 20 (2010) p.180-189

Functional comparison of innate immune signaling pathways in primates.
Barreiro LB, Marioni JC, Blekhman R, Stephens M, Gilad Y.
PLoS genetics Volume 6 (2010) p.e1001249

Genomic-scale capture and sequencing of endogenous DNA from feces.
Perry GH, Marioni JC, Melsted P, Gilad Y.
Molecular ecology Volume 19 (2010) p.5332-5344

Unknown year

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression
Kar G, Kim J, Kolodziejczyk AA, Natarajan K, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA.
Volume (0) p.

Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues
Achim K, Eling N, Martinez Vergara H, Yanina Bertucci P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D.
Volume (0) p.

Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours
Haghverdi L, Lun ATL, Morgan MD, Marioni JC.
Volume (0) p.