Publications by authors named "Alexander van Oudenaarden"

100Publications

An in vitro model of early anteroposterior organization during human development.

Nature 2020 06 11;582(7812):410-415. Epub 2020 Jun 11.

Department of Genetics, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/s41586-020-2383-9DOI Listing
June 2020

Sequencing metabolically labeled transcripts in single cells reveals mRNA turnover strategies.

Science 2020 03;367(6482):1151-1156

Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, Netherlands.

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http://dx.doi.org/10.1126/science.aax3072DOI Listing
March 2020

Publisher Correction: Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids.

Nature 2020 03;579(7799):E11

Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/s41586-020-2113-3DOI Listing
March 2020

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids.

Nature 2020 06 19;582(7812):405-409. Epub 2020 Feb 19.

Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/s41586-020-2024-3DOI Listing
June 2020

Snake Venom Gland Organoids.

Cell 2020 01;180(2):233-247.e21

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, 3584 CT Utrecht, the Netherlands; Oncode Institute, Hubrecht Institute, 3584 CT Utrecht, the Netherlands; The Princess Maxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.11.038DOI Listing
January 2020

Enteroendocrine and tuft cells support Lgr5 stem cells on Paneth cell depletion.

Proc Natl Acad Sci U S A 2019 Dec 16. Epub 2019 Dec 16.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands;

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http://dx.doi.org/10.1073/pnas.1801888117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6936398PMC
December 2019

Unravelling cellular relationships during development and regeneration using genetic lineage tracing.

Nat Rev Mol Cell Biol 2019 12 5;20(12):753-765. Epub 2019 Nov 5.

Oncode Institute, Utrecht, Netherlands.

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http://dx.doi.org/10.1038/s41580-019-0186-3DOI Listing
December 2019

Cell Type Purification by Single-Cell Transcriptome-Trained Sorting.

Cell 2019 10;179(2):527-542.e19

Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands; Oncode Institute, Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6863042PMC
October 2019

A transcriptomic roadmap to α- and β-cell differentiation in the embryonic pancreas.

Development 2019 06 24;146(12). Epub 2019 Jun 24.

Hubrecht Institute/KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands

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http://dx.doi.org/10.1242/dev.173716DOI Listing
June 2019

Spindle checkpoint silencing at kinetochores with submaximal microtubule occupancy.

J Cell Sci 2019 06 17;132(12). Epub 2019 Jun 17.

Oncode Institute, Hubrecht Institute - KNAW and University Medical Centre Utrecht, Utrecht, 3584 CT, The Netherlands

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http://dx.doi.org/10.1242/jcs.231589DOI Listing
June 2019

Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration.

Cell Stem Cell 2019 07 9;25(1):23-38.e8. Epub 2019 May 9.

Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2019.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6814390PMC
July 2019

Combined quantification of intracellular (phospho-)proteins and transcriptomics from fixed single cells.

Sci Rep 2019 02 6;9(1):1469. Epub 2019 Feb 6.

Department of Molecular Developmental Biology, Radboud Institute for Molecular Life Sciences, Science Faculty, Radboud University, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.

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http://dx.doi.org/10.1038/s41598-018-37977-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6365588PMC
February 2019

Spatial Transcriptomics of C. elegans Males and Hermaphrodites Identifies Sex-Specific Differences in Gene Expression Patterns.

Dev Cell 2018 12 8;47(6):801-813.e6. Epub 2018 Nov 8.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15345807183083
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http://dx.doi.org/10.1016/j.devcel.2018.10.016DOI Listing
December 2018

The Majority of CD45 Ter119 CD31 Bone Marrow Cell Fraction Is of Hematopoietic Origin and Contains Erythroid and Lymphoid Progenitors.

Immunity 2018 10 9;49(4):627-639.e6. Epub 2018 Oct 9.

Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, 10461, USA; The Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, 10461, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613183038
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http://dx.doi.org/10.1016/j.immuni.2018.08.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377266PMC
October 2018

Mapping the physical network of cellular interactions.

Nat Methods 2018 07 21;15(7):547-553. Epub 2018 May 21.

Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands.

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http://dx.doi.org/10.1038/s41592-018-0009-zDOI Listing
July 2018

Single-Cell Transcriptomics Meets Lineage Tracing.

Cell Stem Cell 2018 Aug 10;23(2):166-179. Epub 2018 May 10.

Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2018.04.014DOI Listing
August 2018

Blastocyst-like structures generated solely from stem cells.

Nature 2018 05 2;557(7703):106-111. Epub 2018 May 2.

Hubrecht Institute for Developmental Biology and Stem Cell Research, Royal Netherlands Academy of Arts and Sciences (KNAW) and UMC Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/s41586-018-0051-0DOI Listing
May 2018

Whole-organism clone tracing using single-cell sequencing.

Nature 2018 04 28;556(7699):108-112. Epub 2018 Mar 28.

Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.

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http://www.nature.com/doifinder/10.1038/nature25969
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http://dx.doi.org/10.1038/nature25969DOI Listing
April 2018

Single-Cell Sequencing of the Healthy and Diseased Heart Reveals Cytoskeleton-Associated Protein 4 as a New Modulator of Fibroblasts Activation.

Circulation 2018 07 31;138(2):166-180. Epub 2018 Jan 31.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (M.M.G., B.M., H.d.R., S.v.d.E., H.T., D.V., G.P.A.L., A.v.O., E v.R.)

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http://dx.doi.org/10.1161/CIRCULATIONAHA.117.030742DOI Listing
July 2018

Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy.

Proc Natl Acad Sci U S A 2018 01 8;115(4):E610-E619. Epub 2018 Jan 8.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, 3584 CT, Utrecht, The Netherlands;

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http://dx.doi.org/10.1073/pnas.1715911114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5789932PMC
January 2018

A Single-Cell RNA Sequencing Study Reveals Cellular and Molecular Dynamics of the Hippocampal Neurogenic Niche.

Cell Rep 2017 Dec;21(11):3271-3284

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.11.050DOI Listing
December 2017

Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells.

Nat Commun 2017 10 23;8(1):1096. Epub 2017 Oct 23.

Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/s41467-017-01076-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5653659PMC
October 2017

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations.

Nat Methods 2017 09;14(10):935-936

Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1038/nmeth.4437DOI Listing
September 2017

Tomo-Seq Identifies SOX9 as a Key Regulator of Cardiac Fibrosis During Ischemic Injury.

Circulation 2017 Oct 19;136(15):1396-1409. Epub 2017 Jul 19.

From Hubrecht Institute, KNAW (G.P.A.L., J.P.J., M.M.G., B.M., K.T.S., M.V.-G., D.V., H.d.R., M.W.V., M.P.C., A.v.O., E.v.R.), Department of Pathology (M.M.H.H.), Department of Cardiology (N.d.J., E.v.R.), University Medical Center Utrecht, The Netherlands; and Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany (J.P.J.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.117.027832DOI Listing
October 2017

Celebrating 100 years of Developmental Biology at the Hubrecht Institute.

Dev Biol 2017 Aug 6;428(2):259-260. Epub 2017 Jun 6.

Hubrecht Institute - KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1016/j.ydbio.2017.06.001DOI Listing
August 2017

Circadian networks in human embryonic stem cell-derived cardiomyocytes.

EMBO Rep 2017 07 23;18(7):1199-1212. Epub 2017 May 23.

Division of Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands

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http://dx.doi.org/10.15252/embr.201743897DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5494509PMC
July 2017

Identity and dynamics of mammary stem cells during branching morphogenesis.

Nature 2017 02 30;542(7641):313-317. Epub 2017 Jan 30.

Cancer Genomics Netherlands, Hubrecht Institute-KNAW &University Medical Centre Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1038/nature21046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6097610PMC
February 2017

Cdx and T Brachyury Co-activate Growth Signaling in the Embryonic Axial Progenitor Niche.

Cell Rep 2016 12;17(12):3165-3177

Hubrecht Institute and UMC Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.11.069DOI Listing
December 2016

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq.

Cell 2016 Dec;167(7):1883-1896.e15

Department of Immunology, Weizmann Institute, Rehovot 76100, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.11.039DOI Listing
December 2016

Induced Quiescence of Lgr5+ Stem Cells in Intestinal Organoids Enables Differentiation of Hormone-Producing Enteroendocrine Cells.

Cell Stem Cell 2017 02 8;20(2):177-190.e4. Epub 2016 Dec 8.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Uppsalalaan 8, 3584 CT, Utrecht the Netherlands; Cancer Genomics Netherlands, UMC Utrecht, 3584 GC, Utrecht, the Netherlands; Princess Máxima Centre, 3584 CT, Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.11.001DOI Listing
February 2017

A Single-Cell Transcriptome Atlas of the Human Pancreas.

Cell Syst 2016 10 29;3(4):385-394.e3. Epub 2016 Sep 29.

Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2016.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5092539PMC
October 2016

Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon.

Proc Natl Acad Sci U S A 2016 09 29;113(37):E5399-407. Epub 2016 Aug 29.

Hubrecht Institute for Developmental Biology and Stem Cell Research, 3584 CT, Utrecht, The Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX, Utrecht, The Netherlands;

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http://dx.doi.org/10.1073/pnas.1607327113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5027439PMC
September 2016

Patched Receptors Sense, Interpret, and Establish an Epidermal Hedgehog Signaling Gradient.

J Invest Dermatol 2017 01 4;137(1):179-186. Epub 2016 Aug 4.

Division of Molecular Genetics and Development, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia. Electronic address:

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http://dx.doi.org/10.1016/j.jid.2016.06.632DOI Listing
January 2017

Single-cell 5hmC sequencing reveals chromosome-wide cell-to-cell variability and enables lineage reconstruction.

Nat Biotechnol 2016 08 27;34(8):852-6. Epub 2016 Jun 27.

Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, the Netherlands.

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http://dx.doi.org/10.1038/nbt.3598DOI Listing
August 2016

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data.

Cell Stem Cell 2016 08 23;19(2):266-277. Epub 2016 Jun 23.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, 3584 CT Utrecht, the Netherlands; Cancer Genomics Netherlands, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.05.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4985539PMC
August 2016

Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies.

Virology 2016 07 27;494:236-47. Epub 2016 Apr 27.

Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Division of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.virol.2016.04.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5366982PMC
July 2016

Plasticity between Epithelial and Mesenchymal States Unlinks EMT from Metastasis-Enhancing Stem Cell Capacity.

Cell Rep 2016 Mar 3;14(10):2281-8. Epub 2016 Mar 3.

Cancer Genomics Center-Hubrecht Institute-KNAW & University Medical Centre Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2016.02.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4802222PMC
March 2016

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters.

Cell Stem Cell 2016 Feb 28;18(2):203-13. Epub 2016 Jan 28.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2016.01.001DOI Listing
February 2016

Spatially Resolved Genome-wide Transcriptional Profiling Identifies BMP Signaling as Essential Regulator of Zebrafish Cardiomyocyte Regeneration.

Dev Cell 2016 Jan 31;36(1):36-49. Epub 2015 Dec 31.

Hubrecht Institute, University Medical Centre Utrecht, Uppsalaan 8, 3584 CT Utrecht, the Netherlands; Medical Physiology, University Medical Centre Utrecht, Yalelaan 50, 3584 CM Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2015.12.010DOI Listing
January 2016

Studying lineage decision-making in vitro: emerging concepts and novel tools.

Annu Rev Cell Dev Biol 2015 ;31:317-45

Leiden University, 2333 CC Leiden, The Netherlands; email:

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http://dx.doi.org/10.1146/annurev-cellbio-100814-125300DOI Listing
September 2016

Differential Stoichiometry among Core Ribosomal Proteins.

Cell Rep 2015 Nov 22;13(5):865-73. Epub 2015 Oct 22.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.

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http://dx.doi.org/10.1016/j.celrep.2015.09.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644233PMC
November 2015

Design and Analysis of Single-Cell Sequencing Experiments.

Cell 2015 Nov;163(4):799-810

Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584 CT Utrecht, the Netherlands; University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CX Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.10.039DOI Listing
November 2015

A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary.

PLoS Genet 2015 Sep 17;11(9):e1005531. Epub 2015 Sep 17.

Whitehead Institute, Cambridge, Massachusetts, United States of America; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, United States of America.

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http://pagelab.wi.mit.edu/pdf/2015-Soh.pdf
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http://dx.plos.org/10.1371/journal.pgen.1005531
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http://dx.doi.org/10.1371/journal.pgen.1005531DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574967PMC
September 2015

Single-cell messenger RNA sequencing reveals rare intestinal cell types.

Nature 2015 Sep 19;525(7568):251-5. Epub 2015 Aug 19.

Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nature14966DOI Listing
September 2015

DAZL regulates Tet1 translation in murine embryonic stem cells.

EMBO Rep 2015 Jul 15;16(7):791-802. Epub 2015 Jun 15.

Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands Department of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands

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http://dx.doi.org/10.15252/embr.201540538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515119PMC
July 2015

Single-cell transcriptomics enters the age of mass production.

Mol Cell 2015 May;58(4):563-4

Hubrecht Institute-KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.05.019DOI Listing
May 2015

Cells change their sensitivity to an EGF morphogen gradient to control EGF-induced gene expression.

Nat Commun 2015 May 11;6:7053. Epub 2015 May 11.

1] Departments of Physics and Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA [2] Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/ncomms8053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438782PMC
May 2015

Gene expression. MicroRNA control of protein expression noise.

Science 2015 Apr;348(6230):128-32

Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge MA 02139, USA. Department of Biology, MIT, Cambridge, MA 02139, USA. Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences, and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, Netherlands.

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http://dx.doi.org/10.1126/science.aaa1738DOI Listing
April 2015

Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling.

PLoS Genet 2015 Mar 4;11(3):e1005019. Epub 2015 Mar 4.

Whitehead Institute, Cambridge, Massachusetts, United States of America; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1005019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349450PMC
March 2015

Ascl2 acts as an R-spondin/Wnt-responsive switch to control stemness in intestinal crypts.

Cell Stem Cell 2015 Feb 22;16(2):158-70. Epub 2015 Jan 22.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), University Medical Centre Utrecht, CancerGenomiCs.nl, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2014.12.006DOI Listing
February 2015

Integrated genome and transcriptome sequencing of the same cell.

Nat Biotechnol 2015 Mar 19;33(3):285-289. Epub 2015 Jan 19.

Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nbt.3129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374170PMC
March 2015

A predictive model of bifunctional transcription factor signaling during embryonic tissue patterning.

Dev Cell 2014 Nov 24;31(4):448-60. Epub 2014 Nov 24.

Departments of Physics and Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Hubrecht Institute, KNAW, and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2014.10.017DOI Listing
November 2014

Spatially resolved transcriptomics and beyond.

Nat Rev Genet 2015 01 2;16(1):57-66. Epub 2014 Dec 2.

Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nrg3832DOI Listing
January 2015

Genome-wide RNA Tomography in the zebrafish embryo.

Cell 2014 Oct;159(3):662-75

Hubrecht Institute, KNAW and University Medical Center Utrecht, Cancer Genomics Netherlands, 3584 CT Utrecht, the Netherlands; Skolkovo Institute of Science and Technology (Skoltech), Novaya Street 100, Skolkovo Moscow Region 143025, Russia. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2014.09.038DOI Listing
October 2014

Cell intrinsic modulation of Wnt signaling controls neuroblast migration in C. elegans.

Dev Cell 2014 Oct 16;31(2):188-201. Epub 2014 Oct 16.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2014.08.008DOI Listing
October 2014

Constant growth rate can be supported by decreasing energy flux and increasing aerobic glycolysis.

Cell Rep 2014 May 24;7(3):705-14. Epub 2014 Apr 24.

Departments of Physics and Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.03.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4049626PMC
May 2014

Validation of noise models for single-cell transcriptomics.

Nat Methods 2014 Jun 20;11(6):637-40. Epub 2014 Apr 20.

1] Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, The Netherlands. [2] University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/nmeth.2930DOI Listing
June 2014

Transcriptional profiling of cells sorted by RNA abundance.

Nat Methods 2014 May 30;11(5):549-551. Epub 2014 Mar 30.

Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States.

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http://dx.doi.org/10.1038/nmeth.2910DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4174458PMC
May 2014

Every cell is special: genome-wide studies add a new dimension to single-cell biology.

Cell 2014 Mar;157(1):8-11

Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.

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http://dx.doi.org/10.1016/j.cell.2014.02.010DOI Listing
March 2014

Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity.

Cell Rep 2014 Feb 23;6(3):514-27. Epub 2014 Jan 23.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2013.12.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3928845PMC
February 2014

Genetic and phenotypic diversity in breast tumor metastases.

Cancer Res 2014 Mar 21;74(5):1338-48. Epub 2014 Jan 21.

Authors' Affiliations: Departments of Medical Oncology and Biostatistics and Computational Biology, Dana-Farber Cancer Institute; Department of Medicine, Brigham and Women's Hospital; Department of Medicine, Harvard Medical School; Department of Biostatistics, Harvard School of Public Health, Boston; Departments of Physics and Biology, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology; Harvard Stem Cell Institute, Cambridge, Massachusetts; Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, New York; Departments of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Medical Oncology, Hospital Clinic, Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain; Department of Pathology, MizMedi Hospital, Seoul, South Korea; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; and Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Utrecht, the Netherlands.

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http://dx.doi.org/10.1158/0008-5472.CAN-13-2357-TDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963810PMC
March 2014

FuseFISH: robust detection of transcribed gene fusions in single cells.

Cell Rep 2014 Jan 27;6(1):18-23. Epub 2013 Dec 27.

Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2013.12.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4214547PMC
January 2014

Feedback control of gene expression variability in the Caenorhabditis elegans Wnt pathway.

Cell 2013 Nov;155(4):869-80

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1016/j.cell.2013.09.060DOI Listing
November 2013

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins.

Proc Natl Acad Sci U S A 2013 Nov 30;110(46):18602-7. Epub 2013 Oct 30.

Departments of Physics and Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139.

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http://dx.doi.org/10.1073/pnas.1316064110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3831989PMC
November 2013

Dampening of expression oscillations by synchronous regulation of a microRNA and its target.

Nat Genet 2013 Nov 15;45(11):1337-44. Epub 2013 Sep 15.

1] Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [2] Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. [3].

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http://dx.doi.org/10.1038/ng.2763DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3812263PMC
November 2013

Single-molecule mRNA detection and counting in mammalian tissue.

Nat Protoc 2013 Sep 15;8(9):1743-58. Epub 2013 Aug 15.

Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://www.hubrecht.eu/docs/vanoudenaarden/publications/NPRO
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http://www.nature.com/doifinder/10.1038/nprot.2013.109
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http://dx.doi.org/10.1038/nprot.2013.109DOI Listing
September 2013

Stochastic cytokine expression induces mixed T helper cell States.

PLoS Biol 2013 Jul 30;11(7):e1001618. Epub 2013 Jul 30.

Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1001618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3728019PMC
July 2013

Allele-specific detection of single mRNA molecules in situ.

Nat Methods 2013 Sep 11;10(9):869-71. Epub 2013 Aug 11.

Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.2601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789122PMC
September 2013

A physical sciences network characterization of non-tumorigenic and metastatic cells.

Authors:
David B Agus Jenolyn F Alexander Wadih Arap Shashanka Ashili Joseph E Aslan Robert H Austin Vadim Backman Kelly J Bethel Richard Bonneau Wei-Chiang Chen Chira Chen-Tanyolac Nathan C Choi Steven A Curley Matthew Dallas Dhwanil Damania Paul C W Davies Paolo Decuzzi Laura Dickinson Luis Estevez-Salmeron Veronica Estrella Mauro Ferrari Claudia Fischbach Jasmine Foo Stephanie I Fraley Christian Frantz Alexander Fuhrmann Philippe Gascard Robert A Gatenby Yue Geng Sharon Gerecht Robert J Gillies Biana Godin William M Grady Alex Greenfield Courtney Hemphill Barbara L Hempstead Abigail Hielscher W Daniel Hillis Eric C Holland Arig Ibrahim-Hashim Tyler Jacks Roger H Johnson Ahyoung Joo Jonathan E Katz Laimonas Kelbauskas Carl Kesselman Michael R King Konstantinos Konstantopoulos Casey M Kraning-Rush Peter Kuhn Kevin Kung Brian Kwee Johnathon N Lakins Guillaume Lambert David Liao Jonathan D Licht Jan T Liphardt Liyu Liu Mark C Lloyd Anna Lyubimova Parag Mallick John Marko Owen J T McCarty Deirdre R Meldrum Franziska Michor Shannon M Mumenthaler Vivek Nandakumar Thomas V O'Halloran Steve Oh Renata Pasqualini Matthew J Paszek Kevin G Philips Christopher S Poultney Kuldeepsinh Rana Cynthia A Reinhart-King Robert Ros Gregg L Semenza Patti Senechal Michael L Shuler Srimeenakshi Srinivasan Jack R Staunton Yolanda Stypula Hariharan Subramanian Thea D Tlsty Garth W Tormoen Yiider Tseng Alexander van Oudenaarden Scott S Verbridge Jenny C Wan Valerie M Weaver Jonathan Widom Christine Will Denis Wirtz Jonathan Wojtkowiak Pei-Hsun Wu

Sci Rep 2013 ;3:1449

Center for Applied Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.

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http://dx.doi.org/10.1038/srep01449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636513PMC
October 2013

Systematic identification of signal-activated stochastic gene regulation.

Science 2013 Feb;339(6119):584-7

Departments of Physics and Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1126/science.1231456DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3751578PMC
February 2013

Robustness and epistasis in the C. elegans vulval signaling network revealed by pathway dosage modulation.

Dev Cell 2013 Jan;24(1):64-75

Institute of Biology of the Ecole Normale Supérieure, 46 rue d'Ulm, 75230 Paris Cedex 05, France.

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http://dx.doi.org/10.1016/j.devcel.2012.12.001DOI Listing
January 2013

Deconvolving the roles of Wnt ligands and receptors in sensing and amplification.

Mol Syst Biol 2013 ;9:631

Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/msb.2012.64DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564265PMC
September 2013

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

Nat Methods 2013 Feb 23;10(2):122-124. Epub 2012 Dec 23.

Departments of Physics and Biology, and the Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1038/nmeth.2306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3735345PMC
February 2013

Single molecule fluorescent in situ hybridization (smFISH) of C. elegans worms and embryos.

WormBook 2012 Dec 13:1-16. Epub 2012 Dec 13.

Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1895/wormbook.1.153.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4781154PMC
December 2012

Identifying the stem cell of the intestinal crypt: strategies and pitfalls.

Cell Stem Cell 2012 Oct;11(4):452-60

Institute of Medical Biology, 8A Biomedical Grove, Immunos 138648, Singapore.

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http://dx.doi.org/10.1016/j.stem.2012.09.009DOI Listing
October 2012

Dll1+ secretory progenitor cells revert to stem cells upon crypt damage.

Nat Cell Biol 2012 10 23;14(10):1099-1104. Epub 2012 Sep 23.

Hubrecht Institute for Developmental Biology and Stem Cell Research & University Medical Centre Utrecht, Uppsalalaan 8, 3584CT Utrecht, Netherlands.

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http://dx.doi.org/10.1038/ncb2581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789123PMC
October 2012

Transcription of two long noncoding RNAs mediates mating-type control of gametogenesis in budding yeast.

Cell 2012 Sep 6;150(6):1170-81. Epub 2012 Sep 6.

David H. Koch Institute for Integrative Cancer Research and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00928674120093
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http://dx.doi.org/10.1016/j.cell.2012.06.049DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472370PMC
September 2012