John C Marioni

John C Marioni

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John C Marioni

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Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels.

PLoS Genet 2020 Mar 13;16(3):e1008686. Epub 2020 Mar 13.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1008686DOI Listing
March 2020

Toward a Common Coordinate Framework for the Human Body.

Cell 2019 Dec;179(7):1455-1467

New York Genome Center, New York, NY 10013, USA; New York University, Center for Genomics and Systems Biology, New York, NY 10012, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.11.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934046PMC
December 2019

Challenges in measuring and understanding biological noise.

Nat Rev Genet 2019 09;20(9):536-548

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

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http://dx.doi.org/10.1038/s41576-019-0130-6DOI Listing
September 2019

Author Correction: Challenges in measuring and understanding biological noise.

Nat Rev Genet 2019 Sep;20(9):562

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

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http://dx.doi.org/10.1038/s41576-019-0142-2DOI Listing
September 2019

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis.

Nat Commun 2019 03 19;10(1):1251. Epub 2019 Mar 19.

University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1038/s41467-019-09182-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424977PMC
March 2019

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data.

Genome Biol 2019 03 22;20(1):63. Epub 2019 Mar 22.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, UK.

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http://dx.doi.org/10.1186/s13059-019-1662-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6431044PMC
March 2019

Transcriptional Heterogeneity in Naive and Primed Human Pluripotent Stem Cells at Single-Cell Resolution.

Cell Rep 2019 01;26(4):815-824.e4

Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2018.12.099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344340PMC
January 2019

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias.

Elife 2018 10 30;7. Epub 2018 Oct 30.

Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States.

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https://elifesciences.org/articles/36278
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http://dx.doi.org/10.7554/eLife.36278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6277202PMC
October 2018

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data.

Cell Syst 2018 09 29;7(3):284-294.e12. Epub 2018 Aug 29.

The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK; Department of Statistical Science, University College London, 1-19 Torrington Place, London WC1E 7HB, UK; MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XY, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S24054712183027
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http://dx.doi.org/10.1016/j.cels.2018.06.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6167088PMC
September 2018

T cell cytolytic capacity is independent of initial stimulation strength.

Nat Immunol 2018 08 16;19(8):849-858. Epub 2018 Jul 16.

Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/s41590-018-0160-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6300116PMC
August 2018

CTCF maintains regulatory homeostasis of cancer pathways.

Genome Biol 2018 08 7;19(1):106. Epub 2018 Aug 7.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1484-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6081938PMC
August 2018

Detection and removal of barcode swapping in single-cell RNA-seq data.

Nat Commun 2018 07 10;9(1):2667. Epub 2018 Jul 10.

Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, United Kingdom.

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http://dx.doi.org/10.1038/s41467-018-05083-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6039488PMC
July 2018

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.

Nat Biotechnol 2018 06 2;36(5):421-427. Epub 2018 Apr 2.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

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http://www.nature.com/doifinder/10.1038/nbt.4091
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http://dx.doi.org/10.1038/nbt.4091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6152897PMC
June 2018

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

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

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

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

CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

Genome Biol 2018 06 26;19(1):81. Epub 2018 Jun 26.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-018-1461-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6020341PMC
June 2018

Using single-cell genomics to understand developmental processes and cell fate decisions.

Mol Syst Biol 2018 04 16;14(4):e8046. Epub 2018 Apr 16.

Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5900446PMC
http://dx.doi.org/10.15252/msb.20178046DOI Listing
April 2018

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells.

Stem Cell Reports 2017 12 16;9(6):1898-1915. Epub 2017 Nov 16.

Stem Cells and Regenerative Medicine Section, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, UK. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2017.10.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5785701PMC
December 2017

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos.

Nature 2017 12 29;552(7684):239-243. Epub 2017 Nov 29.

Mammalian Embryo and Stem Cell Group, University of Cambridge, Department of Physiology, Development and Neuroscience, Downing Street, Cambridge CB2 3EG, UK.

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http://dx.doi.org/10.1038/nature24675DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5768241PMC
December 2017

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing.

Nat Commun 2017 12 11;8(1):2128. Epub 2017 Dec 11.

Department of Pharmacology, University of Cambridge, Cambridge, CB2 1PD, UK.

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http://dx.doi.org/10.1038/s41467-017-02001-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5723634PMC
December 2017

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data.

Genome Res 2017 11 13;27(11):1795-1806. Epub 2017 Oct 13.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, United Kingdom.

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http://dx.doi.org/10.1101/gr.222877.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5668938PMC
November 2017

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

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

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

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

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data.

BMC Genomics 2017 Nov 25;18(1):904. Epub 2017 Nov 25.

Cancer Research UK Cambridge Institute, University of Cambridge, CB2 0RE, Cambridge, UK.

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http://dx.doi.org/10.1186/s12864-017-4253-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702132PMC
November 2017

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology.

Annu Rev Cell Dev Biol 2017 10 16;33:537-553. Epub 2017 Aug 16.

Developmental Biology Unit, EMBL, 69117 Heidelberg, Germany; email:

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http://dx.doi.org/10.1146/annurev-cellbio-100616-060818DOI Listing
October 2017

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

Nat Commun 2017 10 23;8(1):1092. Epub 2017 Oct 23.

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

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http://dx.doi.org/10.1038/s41467-017-01037-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653656PMC
October 2017

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation.

Cell Rep 2017 08;20(5):1215-1228

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

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http://dx.doi.org/10.1016/j.celrep.2017.07.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5554778PMC
August 2017

Impact of Alternative Splicing on the Human Proteome.

Cell Rep 2017 08;20(5):1229-1241

The Medical Research Council Cancer Unit, University of Cambridge, Cambridge CB2 0XZ, UK; RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.07.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5554779PMC
August 2017

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data.

Biostatistics 2017 Jul;18(3):451-464

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1093/biostatistics/kxw055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862359PMC
July 2017

Testing for differential abundance in mass cytometry data.

Nat Methods 2017 Jul 15;14(7):707-709. Epub 2017 May 15.

Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/nmeth.4295DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6155493PMC
July 2017

Normalizing single-cell RNA sequencing data: challenges and opportunities.

Nat Methods 2017 Jun 15;14(6):565-571. Epub 2017 May 15.

EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/nmeth.4292DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5549838PMC
June 2017

Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

Nat Commun 2017 06 26;8(1):36. Epub 2017 Jun 26.

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

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http://dx.doi.org/10.1038/s41467-017-00052-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484669PMC
June 2017

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.

Elife 2017 03 21;6. Epub 2017 Mar 21.

Wellcome Trust/Cancer Research United Kingdom Gurdon Institute, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.7554/eLife.22345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404928PMC
March 2017

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

F1000Res 2016 31;5:2122. Epub 2016 Aug 31.

Cancer Research UK Cambridge Institute, Cambridge, UK; EMBL European Bioinformatics Institute, Cambridge, UK; Wellcome Trust Sanger Institute, Cambridge, UK.

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http://dx.doi.org/10.12688/f1000research.9501.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5112579PMC
August 2016

HDTD: analyzing multi-tissue gene expression data.

Bioinformatics 2016 07 7;32(14):2193-5. Epub 2016 Jun 7.

CRUK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK.

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http://dx.doi.org/10.1093/bioinformatics/btw224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937203PMC
July 2016

Resolving early mesoderm diversification through single-cell expression profiling.

Nature 2016 07 6;535(7611):289-293. Epub 2016 Jul 6.

Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/nature18633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947525PMC
July 2016

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System.

PLoS One 2015 4;10(9):e0137367. Epub 2015 Sep 4.

University of Cambridge, Cancer Research UK - Cambridge Institute, Li Ka Shing Centre, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137367PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4560434PMC
May 2016

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

PLoS Genet 2016 05 11;12(5):e1006024. Epub 2016 May 11.

University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1006024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4864286PMC
May 2016

Beyond comparisons of means: understanding changes in gene expression at the single-cell level.

Genome Biol 2016 Apr 15;17:70. Epub 2016 Apr 15.

EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1186/s13059-016-0930-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4832562PMC
April 2016

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

Genome Biol 2016 Apr 27;17:75. Epub 2016 Apr 27.

Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, CB2 0RE, Cambridge, UK.

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http://dx.doi.org/10.1186/s13059-016-0947-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4848819PMC
April 2016

Structure and evolutionary history of a large family of NLR proteins in the zebrafish.

Open Biol 2016 Apr 27;6(4):160009. Epub 2016 Apr 27.

Institut für Genetik, Universität zu Köln, Köln, Germany The European Molecular Biology Laboratory, Heidelberg, Germany

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http://dx.doi.org/10.1098/rsob.160009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4852459PMC
April 2016

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

Cell 2016 Mar;165(1):61-74

Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.01.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4819611PMC
March 2016

Classification of low quality cells from single-cell RNA-seq data.

Genome Biol 2016 Feb 17;17:29. Epub 2016 Feb 17.

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

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http://dx.doi.org/10.1186/s13059-016-0888-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758103PMC
February 2016

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq.

Sci Rep 2015 Dec 16;5:18178. Epub 2015 Dec 16.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton-Cambridge, CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1038/srep18178DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4680959PMC
December 2015

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

Cell Stem Cell 2015 Oct;17(4):471-85

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595712PMC
October 2015

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Nat Commun 2015 Oct 22;6:8687. Epub 2015 Oct 22.

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

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http://dx.doi.org/10.1038/ncomms9687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627577PMC
October 2015

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

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

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

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

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.

PLoS Comput Biol 2015 Jun 24;11(6):e1004333. Epub 2015 Jun 24.

MRC Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480965PMC
June 2015

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse.

Sci Rep 2015 Jun 25;5:11487. Epub 2015 Jun 25.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton-Cambridge, CB10 1SA, United Kingdom.

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http://dx.doi.org/10.1038/srep11487DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480006PMC
June 2015

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin.

Nat Biotechnol 2015 May 13;33(5):503-9. Epub 2015 Apr 13.

1] European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK. [2] Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. [3] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK.

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http://dx.doi.org/10.1038/nbt.3209DOI Listing
May 2015

The technology and biology of single-cell RNA sequencing.

Mol Cell 2015 May;58(4):610-20

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address:

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http://www.cell.com/molecular-cell/pdf/S1097-2765(15)00261-0
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http://dx.doi.org/10.1016/j.molcel.2015.04.005DOI Listing
May 2015

Testing the mean matrix in high-dimensional transposable data.

Biometrics 2015 Mar 23;71(1):157-166. Epub 2015 Jan 23.

EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, U.K.

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http://dx.doi.org/10.1111/biom.12257DOI Listing
March 2015

Computational and analytical challenges in single-cell transcriptomics.

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

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

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

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

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

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

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

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

Cell Rep 2014 Dec 12;9(6):1990-2000. Epub 2014 Dec 12.

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

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http://dx.doi.org/10.1016/j.celrep.2014.11.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542306PMC
December 2014

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis.

Nat Genet 2014 Jul 25;46(7):753-8. Epub 2014 May 25.

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

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http://dx.doi.org/10.1038/ng.2971DOI Listing
July 2014

Random monoallelic gene expression increases upon embryonic stem cell differentiation.

Dev Cell 2014 Feb;28(4):351-65

Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA; Watson School of Biological Sciences, Cold Spring Harbor Laboratory, One Bungtown Road, Cold Spring Harbor, NY 11724, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2014.01.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3955261PMC
February 2014

bioWeb3D: an online webGL 3D data visualisation tool.

BMC Bioinformatics 2013 Jun 7;14:185. Epub 2013 Jun 7.

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

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http://dx.doi.org/10.1186/1471-2105-14-185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3710502PMC
June 2013

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

Proc Natl Acad Sci U S A 2013 Mar 14;110(10):4009-14. Epub 2013 Feb 14.

Department of Oncology, University of Cambridge, Cambridge CB2 2XZ, United Kingdom.

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http://dx.doi.org/10.1073/pnas.1219747110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3593922PMC
March 2013

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression.

Genome Res 2012 Dec 23;22(12):2376-84. Epub 2012 Aug 23.

European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom.

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http://dx.doi.org/10.1101/gr.142281.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514667PMC
December 2012

Tools for mapping high-throughput sequencing data.

Bioinformatics 2012 Dec 11;28(24):3169-77. Epub 2012 Oct 11.

EMBL Outstation, European Bioinformatics Institute (EBI), Hinxton, Cambridge CB10 ISD, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts605DOI Listing
December 2012

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection.

Proc Natl Acad Sci U S A 2012 Jan 10;109(4):1204-9. Epub 2012 Jan 10.

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1073/pnas.1115761109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3268270PMC
January 2012

Gene expression differences among primates are associated with changes in a histone epigenetic modification.

Genetics 2011 Apr 14;187(4):1225-34. Epub 2011 Feb 14.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1534/genetics.110.126177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070530PMC
April 2011

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

PLoS Genet 2011 Feb 24;7(2):e1001316. Epub 2011 Feb 24.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1001316DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3044686PMC
February 2011

Genomic-scale capture and sequencing of endogenous DNA from feces.

Mol Ecol 2010 Dec 3;19(24):5332-44. Epub 2010 Nov 3.

Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1111/j.1365-294X.2010.04888.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2998560PMC
December 2010

Functional comparison of innate immune signaling pathways in primates.

PLoS Genet 2010 Dec 16;6(12):e1001249. Epub 2010 Dec 16.

Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

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https://dx.plos.org/10.1371/journal.pgen.1001249
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http://dx.doi.org/10.1371/journal.pgen.1001249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3002988PMC
December 2010

Sex-specific and lineage-specific alternative splicing in primates.

Genome Res 2010 Feb 15;20(2):180-9. Epub 2009 Dec 15.

Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA.

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http://dx.doi.org/10.1101/gr.099226.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2813474PMC
February 2010

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data.

Bioinformatics 2009 Dec 6;25(24):3207-12. Epub 2009 Oct 6.

Department of Human Genetics, University of Chicago, 920 E. 58th St., CLSC 507, Chicago, IL 60637, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2788925PMC
December 2009

The pitfalls of platform comparison: DNA copy number array technologies assessed.

BMC Genomics 2009 Dec 8;10:588. Epub 2009 Dec 8.

Department of Oncology, University of Cambridge, Addenbrooke's Hopsital, Hills Road, Cambridge CB20XZ, UK.

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http://dx.doi.org/10.1186/1471-2164-10-588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2797821PMC
December 2009

Hidden copy number variation in the HapMap population.

Proc Natl Acad Sci U S A 2008 Jul 15;105(29):10067-72. Epub 2008 Jul 15.

Department of Oncology, Computational Biology Group, University of Cambridge, Cancer Research UK Cambridge Research Institute, Robinson Way, Cambridge, United Kingdom.

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http://dx.doi.org/10.1073/pnas.0711252105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2481329PMC
July 2008