Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis
Ernst C, Eling N, Martinez-Jimenez CP, Marioni JC, Odom DT. Preprint DOI: 10.1101/350868
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
Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body.
Achim K, Eling N, Vergara HM, Bertucci PY, Musser J, Vopalensky P, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Molecular biology and evolution Volume 35 (2018) p.1047-1062 DOI: 10.1093/molbev/msx336
Using single-cell genomics to understand developmental processes and cell fate decisions.
Griffiths JA, Scialdone A, Marioni JC. Molecular systems biology Volume 14 (2018) p.e8046 DOI: 10.15252/msb.20178046
Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data
Lun A, Riesenfeld S, Andrews T, Dao TP, Gomes T, Marioni J, participants in the 1st Human Cell Atlas Jamboree. Preprint DOI: 10.1101/234872
Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Nature biotechnology Volume 36 (2018) p.421-427 DOI: 10.1038/nbt.4091
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
Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.
Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC. Nature cell biology Volume 20 (2018) p.127-134 DOI: 10.1038/s41556-017-0013-z


Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis
Stojic L, Lun A, Mangei J, Mascalchi P, Quarantotti V, Barr A, Bakal C, Marioni J, Gergely F, Odom D. Preprint DOI: 10.1101/234930
Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.
Shahbazi MN, Scialdone A, Skorupska N, Weberling A, Recher G, Zhu M, Jedrusik A, Devito LG, Noli L, Macaulay IC, Buecker C, Khalaf Y, Ilic D, Voet T, Marioni JC, Zernicka-Goetz M. Nature Volume 552 (2017) p.239-243 DOI: 10.1038/nature24675
Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.
Griffiths JA, Scialdone A, Marioni JC. BMC genomics Volume 18 (2017) p.904 DOI: 10.1186/s12864-017-4253-x
Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.
Welby E, Lakowski J, Di Foggia V, Budinger D, Gonzalez-Cordero A, Lun ATL, Epstein M, Patel A, Cuevas E, Kruczek K, Naeem A, Minneci F, Hubank M, Jones DT, Marioni JC, Ali RR, Sowden JC. Stem cell reports Volume 9 (2017) p.1898-1915 DOI: 10.1016/j.stemcr.2017.10.018
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
Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.
Wong ES, Schmitt BM, Kazachenka A, Thybert D, Redmond A, Connor F, Rayner TF, Feig C, Ferguson-Smith AC, Marioni JC, Odom DT, Flicek P. Nature communications Volume 8 (2017) p.1092 DOI: 10.1038/s41467-017-01037-x
How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.
Marioni JC, Arendt D. Annual review of cell and developmental biology Volume 33 (2017) p.537-553 DOI: 10.1146/annurev-cellbio-100616-060818
Detection and removal of barcode swapping in single-cell RNA-seq data
Griffiths JA, Richard AC, Bach K, Lun AT, Marioni JC. Preprint DOI: 10.1101/177048
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 DOI: 10.1016/j.celrep.2017.07.009
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 DOI: 10.1016/j.celrep.2017.07.025
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, Bertucci PY, Brunet T, Collier P, Benes V, Marioni JC, Arendt D. Preprint DOI: 10.1101/167742
Correcting batch effects in single-cell RNA sequencing data by matching mutual nearest neighbours.
Haghverdi L, Lun ATL, Morgan MD, Marioni JC. Preprint DOI: 10.1101/165118
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 DOI: 10.1038/nmeth.4292
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) DOI: 10.7554/eLife.22345
Adipocyte Accumulation in the Bone Marrow during Obesity and Aging Impairs Stem Cell-Based Hematopoietic and Bone Regeneration.
Ambrosi TH, Scialdone A, Graja A, Gohlke S, Jank AM, Bocian C, Woelk L, Fan H, Logan DW, Schürmann A, Saraiva LR, Schulz TJ. Cell stem cell Volume 20 (2017) p.771-784.e6 DOI: 10.1016/j.stem.2017.02.009
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Triglia ET, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Preprint DOI: 10.1101/117267


Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data
Lun AT, Marioni JC. Preprint DOI: 10.1101/073973
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
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 DOI: 10.1038/nature18633
HDTD: analyzing multi-tissue gene expression data.
Touloumis A, Marioni JC, Tavaré S. Bioinformatics (Oxford, England) Volume 32 (2016) p.2193-2195 DOI: 10.1093/bioinformatics/btw224
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 DOI: 10.1371/journal.pgen.1006024
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 DOI: 10.1098/rsob.160009
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 DOI: 10.1186/s13059-016-0930-3
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 DOI: 10.1016/j.cell.2016.01.047
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 DOI: 10.1038/ncomms10415
Beyond comparisons of means: understanding changes in gene expression at the single-cell level
Vallejos CA, Richardson S, Marioni JC. Preprint DOI: 10.1101/035949


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 DOI: 10.1038/srep18178
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 DOI: 10.1038/ncomms9687
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 DOI: 10.1016/j.stem.2015.09.011
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 DOI: 10.1186/s13059-015-0749-3
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 DOI: 10.1371/journal.pone.0137367
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 J, Soylemez O, Kondrashov F, Leptin M. Preprint DOI: 10.1101/022061
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
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 DOI: 10.1038/srep11487
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Vallejos CA, Marioni JC, Richardson S. PLoS computational biology Volume 11 (2015) p.e1004333 DOI: 10.1371/journal.pcbi.1004333
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 DOI: 10.1016/j.molcel.2015.04.005
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 DOI: 10.1038/nbt.3209
How plants manage food reserves at night: quantitative models and open questions.
Scialdone A, Howard M. Frontiers in plant science Volume 6 (2015) p.204 DOI: 10.3389/fpls.2015.00204
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
Testing the mean matrix in high-dimensional transposable data.
Touloumis A, Tavaré S, Marioni JC. Biometrics Volume 71 (2015) p.157-166 DOI: 10.1111/biom.12257
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
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 DOI: 10.2174/1568009615666150512102957


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 DOI: 10.1016/j.celrep.2014.11.034
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 DOI: 10.1158/0008-5472.CAN-13-3131
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 DOI: 10.1186/s13059-014-0496-x
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 DOI: 10.7554/eLife.02626
RNA-Seq gene profiling--a systematic empirical comparison.
Fonseca NA, Marioni J, Brazma A. PloS one Volume 9 (2014) p.e107026 DOI: 10.1371/journal.pone.0107026
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 DOI: 10.1371/journal.pcbi.1003824
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 DOI: 10.1101/gr.176784.114
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 DOI: 10.1038/ng.2971
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 DOI: 10.1016/j.devcel.2014.01.017


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 DOI: 10.1093/nar/gkt1270
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 DOI: 10.1038/nmeth.2645
Organizing a PhD symposium--an inside view. Setting up a scientific meeting is challenging--a PhD symposium offers its own unique opportunities and pitfalls.
Schröder MS, Harnett D, Minke BA, Nair PS, Committee Member Consortium. EMBO reports Volume 14 (2013) p.856-860 DOI: 10.1038/embor.2013.147
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 DOI: 10.1016/j.cell.2013.07.007
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 DOI: 10.1038/bjc.2013.396
Polymer models of chromatin organization.
Barbieri M, Scialdone A, Piccolo A, Chiariello AM, di Lanno C, Prisco A, Pombo A, Nicodemi M. Frontiers in Genetics Volume 4 (2013) p.113 DOI: 10.3389/fgene.2013.00113
bioWeb3D: an online webGL 3D data visualisation tool.
Pettit JB, Marioni JC. BMC bioinformatics Volume 14 (2013) p.185 DOI: 10.1186/1471-2105-14-185
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 DOI: 10.1073/pnas.1219747110
Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim JK, Marioni JC. Genome biology Volume 14 (2013) p.R7 DOI: 10.1186/gb-2013-14-1-r7


Tools for mapping high-throughput sequencing data.
Fonseca NA, Rung J, Brazma A, Marioni JC. Bioinformatics (Oxford, England) Volume 28 (2012) p.3169-3177 DOI: 10.1093/bioinformatics/bts605
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 DOI: 10.1101/gr.142281.112
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 DOI: 10.1073/pnas.1115761109


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 DOI: 10.1101/gr.130468.111
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 DOI: 10.1093/bioinformatics/btr330
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 DOI: 10.1136/gut.2010.234179
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 DOI: 10.1371/journal.pgen.1001316
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 DOI: 10.1534/genetics.110.126177


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 DOI: 10.1371/journal.pgen.1001249
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 DOI: 10.1111/j.1365-294X.2010.04888.x
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 DOI: 10.1038/nature08872


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 DOI: 10.1101/gr.099226.109