Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 162

1.

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

Gerlach JP, van Buggenum JAG, Tanis SEJ, Hogeweg M, Heuts BMH, Muraro MJ, Elze L, Rivello F, Rakszewska A, van Oudenaarden A, Huck WTS, Stunnenberg HG, Mulder KW.

Sci Rep. 2019 Feb 6;9(1):1469. doi: 10.1038/s41598-018-37977-7.

2.

Correction: Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics (doi: 10.1242/dev.166728).

Attardi A, Fulton T, Florescu M, Shah G, Muresan L, Lenz MO, Lancaster C, Huisken J, van Oudenaarden A, Steventon B.

Development. 2019 Jan 22;146(2). pii: dev175620. doi: 10.1242/dev.175620. No abstract available.

3.

Long-term expanding human airway organoids for disease modeling.

Sachs N, Papaspyropoulos A, Zomer-van Ommen DD, Heo I, Böttinger L, Klay D, Weeber F, Huelsz-Prince G, Iakobachvili N, Amatngalim GD, de Ligt J, van Hoeck A, Proost N, Viveen MC, Lyubimova A, Teeven L, Derakhshan S, Korving J, Begthel H, Dekkers JF, Kumawat K, Ramos E, van Oosterhout MF, Offerhaus GJ, Wiener DJ, Olimpio EP, Dijkstra KK, Smit EF, van der Linden M, Jaksani S, van de Ven M, Jonkers J, Rios AC, Voest EE, van Moorsel CH, van der Ent CK, Cuppen E, van Oudenaarden A, Coenjaerts FE, Meyaard L, Bont LJ, Peters PJ, Tans SJ, van Zon JS, Boj SF, Vries RG, Beekman JM, Clevers H.

EMBO J. 2019 Feb 15;38(4). pii: e100300. doi: 10.15252/embj.2018100300. Epub 2019 Jan 14.

4.

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

Ebbing A, Vértesy Á, Betist MC, Spanjaard B, Junker JP, Berezikov E, van Oudenaarden A, Korswagen HC.

Dev Cell. 2018 Dec 17;47(6):801-813.e6. doi: 10.1016/j.devcel.2018.10.016. Epub 2018 Nov 8.

PMID:
30416013
5.

Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics.

Attardi A, Fulton T, Florescu M, Shah G, Muresan L, Lenz MO, Lancaster C, Huisken J, van Oudenaarden A, Steventon B.

Development. 2018 Nov 9;145(21). pii: dev166728. doi: 10.1242/dev.166728. Erratum in: Development. 2019 Jan 22;146(2):.

6.

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

Boulais PE, Mizoguchi T, Zimmerman S, Nakahara F, Vivié J, Mar JC, van Oudenaarden A, Frenette PS.

Immunity. 2018 Oct 16;49(4):627-639.e6. doi: 10.1016/j.immuni.2018.08.019. Epub 2018 Oct 9.

PMID:
30314756
7.

Single-cell analysis reveals that stochasticity and paracrine signaling control interferon-alpha production by plasmacytoid dendritic cells.

Wimmers F, Subedi N, van Buuringen N, Heister D, Vivié J, Beeren-Reinieren I, Woestenenk R, Dolstra H, Piruska A, Jacobs JFM, van Oudenaarden A, Figdor CG, Huck WTS, de Vries IJM, Tel J.

Nat Commun. 2018 Aug 20;9(1):3317. doi: 10.1038/s41467-018-05784-3.

8.

Tdrd6a Regulates the Aggregation of Buc into Functional Subcellular Compartments that Drive Germ Cell Specification.

Roovers EF, Kaaij LJT, Redl S, Bronkhorst AW, Wiebrands K, de Jesus Domingues AM, Huang HY, Han CT, Riemer S, Dosch R, Salvenmoser W, Grün D, Butter F, van Oudenaarden A, Ketting RF.

Dev Cell. 2018 Aug 6;46(3):285-301.e9. doi: 10.1016/j.devcel.2018.07.009.

9.

Single-cell transcriptomics reveal the dynamic of haematopoietic stem cell production in the aorta.

Baron CS, Kester L, Klaus A, Boisset JC, Thambyrajah R, Yvernogeau L, Kouskoff V, Lacaud G, van Oudenaarden A, Robin C.

Nat Commun. 2018 Jun 28;9(1):2517. doi: 10.1038/s41467-018-04893-3.

10.

Mapping the physical network of cellular interactions.

Boisset JC, Vivié J, Grün D, Muraro MJ, Lyubimova A, van Oudenaarden A.

Nat Methods. 2018 Jul;15(7):547-553. doi: 10.1038/s41592-018-0009-z. Epub 2018 May 21.

PMID:
29786092
11.

Parental haplotype-specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells.

Vértesy Á, Arindrarto W, Roost MS, Reinius B, Torrens-Juaneda V, Bialecka M, Moustakas I, Ariyurek Y, Kuijk E, Mei H, Sandberg R, van Oudenaarden A, Chuva de Sousa Lopes SM.

Nat Commun. 2018 May 14;9(1):1873. doi: 10.1038/s41467-018-04215-7.

12.

Single-Cell Transcriptomics Meets Lineage Tracing.

Kester L, van Oudenaarden A.

Cell Stem Cell. 2018 Aug 2;23(2):166-179. doi: 10.1016/j.stem.2018.04.014. Epub 2018 May 10. Review.

PMID:
29754780
13.

Blastocyst-like structures generated solely from stem cells.

Rivron NC, Frias-Aldeguer J, Vrij EJ, Boisset JC, Korving J, Vivié J, Truckenmüller RK, van Oudenaarden A, van Blitterswijk CA, Geijsen N.

Nature. 2018 May;557(7703):106-111. doi: 10.1038/s41586-018-0051-0. Epub 2018 May 2.

PMID:
29720634
14.

A Caenorhabditis elegans protein with a PRDM9-like SET domain localizes to chromatin-associated foci and promotes spermatocyte gene expression, sperm production and fertility.

Engert CG, Droste R, van Oudenaarden A, Horvitz HR.

PLoS Genet. 2018 Apr 27;14(4):e1007295. doi: 10.1371/journal.pgen.1007295. eCollection 2018 Apr.

15.

Whole-organism clone tracing using single-cell sequencing.

Alemany A, Florescu M, Baron CS, Peterson-Maduro J, van Oudenaarden A.

Nature. 2018 Apr 5;556(7699):108-112. doi: 10.1038/nature25969. Epub 2018 Mar 28.

PMID:
29590089
16.

Expansion of Adult Human Pancreatic Tissue Yields Organoids Harboring Progenitor Cells with Endocrine Differentiation Potential.

Loomans CJM, Williams Giuliani N, Balak J, Ringnalda F, van Gurp L, Huch M, Boj SF, Sato T, Kester L, de Sousa Lopes SMC, Roost MS, Bonner-Weir S, Engelse MA, Rabelink TJ, Heimberg H, Vries RGJ, van Oudenaarden A, Carlotti F, Clevers H, de Koning EJP.

Stem Cell Reports. 2018 Mar 13;10(3):712-724. doi: 10.1016/j.stemcr.2018.02.005.

17.

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

Gladka MM, Molenaar B, de Ruiter H, van der Elst S, Tsui H, Versteeg D, Lacraz GPA, Huibers MMH, van Oudenaarden A, van Rooij E.

Circulation. 2018 Jul 10;138(2):166-180. doi: 10.1161/CIRCULATIONAHA.117.030742. Epub 2018 Jan 31.

PMID:
29386203
18.

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

Basak O, Krieger TG, Muraro MJ, Wiebrands K, Stange DE, Frias-Aldeguer J, Rivron NC, van de Wetering M, van Es JH, van Oudenaarden A, Simons BD, Clevers H.

Proc Natl Acad Sci U S A. 2018 Jan 23;115(4):E610-E619. doi: 10.1073/pnas.1715911114. Epub 2018 Jan 8.

19.

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

Artegiani B, Lyubimova A, Muraro M, van Es JH, van Oudenaarden A, Clevers H.

Cell Rep. 2017 Dec 12;21(11):3271-3284. doi: 10.1016/j.celrep.2017.11.050.

20.

The Human Cell Atlas.

Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe'er D, Phillipakis A, Ponting CP, Quake S, Reik W, Rozenblatt-Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N; Human Cell Atlas Meeting Participants.

Elife. 2017 Dec 5;6. pii: e27041. doi: 10.7554/eLife.27041.

21.

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

Semrau S, Goldmann JE, Soumillon M, Mikkelsen TS, Jaenisch R, van Oudenaarden A.

Nat Commun. 2017 Oct 23;8(1):1096. doi: 10.1038/s41467-017-01076-4.

22.

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

van den Brink SC, Sage F, Vértesy Á, Spanjaard B, Peterson-Maduro J, Baron CS, Robin C, van Oudenaarden A.

Nat Methods. 2017 Sep 29;14(10):935-936. doi: 10.1038/nmeth.4437. No abstract available.

PMID:
28960196
23.

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

Lacraz GPA, Junker JP, Gladka MM, Molenaar B, Scholman KT, Vigil-Garcia M, Versteeg D, de Ruiter H, Vermunt MW, Creyghton MP, Huibers MMH, de Jonge N, van Oudenaarden A, van Rooij E.

Circulation. 2017 Oct 10;136(15):1396-1409. doi: 10.1161/CIRCULATIONAHA.117.027832. Epub 2017 Jul 19.

PMID:
28724751
24.

Celebrating 100 years of Developmental Biology at the Hubrecht Institute.

den Hertog J, van Oudenaarden A.

Dev Biol. 2017 Aug 15;428(2):259-260. doi: 10.1016/j.ydbio.2017.06.001. Epub 2017 Jun 6. No abstract available.

25.

Circadian networks in human embryonic stem cell-derived cardiomyocytes.

Dierickx P, Vermunt MW, Muraro MJ, Creyghton MP, Doevendans PA, van Oudenaarden A, Geijsen N, Van Laake LW.

EMBO Rep. 2017 Jul;18(7):1199-1212. doi: 10.15252/embr.201743897. Epub 2017 May 23.

26.

Identity and dynamics of mammary stem cells during branching morphogenesis.

Scheele CL, Hannezo E, Muraro MJ, Zomer A, Langedijk NS, van Oudenaarden A, Simons BD, van Rheenen J.

Nature. 2017 Feb 16;542(7641):313-317. doi: 10.1038/nature21046. Epub 2017 Jan 30.

27.

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

Amin S, Neijts R, Simmini S, van Rooijen C, Tan SC, Kester L, van Oudenaarden A, Creyghton MP, Deschamps J.

Cell Rep. 2016 Dec 20;17(12):3165-3177. doi: 10.1016/j.celrep.2016.11.069.

28.

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

Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H, David E, Salame TM, Tanay A, van Oudenaarden A, Amit I.

Cell. 2016 Dec 15;167(7):1883-1896.e15. doi: 10.1016/j.cell.2016.11.039.

29.

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

Basak O, Beumer J, Wiebrands K, Seno H, van Oudenaarden A, Clevers H.

Cell Stem Cell. 2017 Feb 2;20(2):177-190.e4. doi: 10.1016/j.stem.2016.11.001. Epub 2016 Dec 8.

30.

A Single-Cell Transcriptome Atlas of the Human Pancreas.

Muraro MJ, Dharmadhikari G, Grün D, Groen N, Dielen T, Jansen E, van Gurp L, Engelse MA, Carlotti F, de Koning EJ, van Oudenaarden A.

Cell Syst. 2016 Oct 26;3(4):385-394.e3. doi: 10.1016/j.cels.2016.09.002. Epub 2016 Sep 29.

31.

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

Sasaki N, Sachs N, Wiebrands K, Ellenbroek SI, Fumagalli A, Lyubimova A, Begthel H, van den Born M, van Es JH, Karthaus WR, Li VS, López-Iglesias C, Peters PJ, van Rheenen J, van Oudenaarden A, Clevers H.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):E5399-407. doi: 10.1073/pnas.1607327113. Epub 2016 Aug 29.

32.

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

Adolphe C, Junker JP, Lyubimova A, van Oudenaarden A, Wainwright B.

J Invest Dermatol. 2017 Jan;137(1):179-186. doi: 10.1016/j.jid.2016.06.632. Epub 2016 Aug 4.

33.

Tomo-seq: A method to obtain genome-wide expression data with spatial resolution.

Kruse F, Junker JP, van Oudenaarden A, Bakkers J.

Methods Cell Biol. 2016;135:299-307. doi: 10.1016/bs.mcb.2016.01.006. Epub 2016 Feb 26.

PMID:
27443932
34.

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

Mooijman D, Dey SS, Boisset JC, Crosetto N, van Oudenaarden A.

Nat Biotechnol. 2016 Aug;34(8):852-6. doi: 10.1038/nbt.3598. Epub 2016 Jun 27.

PMID:
27347753
35.

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

Grün D, Muraro MJ, Boisset JC, Wiebrands K, Lyubimova A, Dharmadhikari G, van den Born M, van Es J, Jansen E, Clevers H, de Koning EJP, van Oudenaarden A.

Cell Stem Cell. 2016 Aug 4;19(2):266-277. doi: 10.1016/j.stem.2016.05.010. Epub 2016 Jun 23.

36.

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

Ramanan V, Trehan K, Ong ML, Luna JM, Hoffmann HH, Espiritu C, Sheahan TP, Chandrasekar H, Schwartz RE, Christine KS, Rice CM, van Oudenaarden A, Bhatia SN.

Virology. 2016 Jul;494:236-47. doi: 10.1016/j.virol.2016.04.020. Epub 2016 Apr 27.

37.

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

Beerling E, Seinstra D, de Wit E, Kester L, van der Velden D, Maynard C, Schäfer R, van Diest P, Voest E, van Oudenaarden A, Vrisekoop N, van Rheenen J.

Cell Rep. 2016 Mar 15;14(10):2281-8. doi: 10.1016/j.celrep.2016.02.034. Epub 2016 Mar 3.

38.

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

Tetteh PW, Basak O, Farin HF, Wiebrands K, Kretzschmar K, Begthel H, van den Born M, Korving J, de Sauvage F, van Es JH, van Oudenaarden A, Clevers H.

Cell Stem Cell. 2016 Feb 4;18(2):203-13. doi: 10.1016/j.stem.2016.01.001. Epub 2016 Jan 28.

39.

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

Wu CC, Kruse F, Vasudevarao MD, Junker JP, Zebrowski DC, Fischer K, Noël ES, Grün D, Berezikov E, Engel FB, van Oudenaarden A, Weidinger G, Bakkers J.

Dev Cell. 2016 Jan 11;36(1):36-49. doi: 10.1016/j.devcel.2015.12.010. Epub 2015 Dec 31.

40.

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

Semrau S, van Oudenaarden A.

Annu Rev Cell Dev Biol. 2015;31:317-45. doi: 10.1146/annurev-cellbio-100814-125300. Review.

PMID:
26566114
41.

Differential Stoichiometry among Core Ribosomal Proteins.

Slavov N, Semrau S, Airoldi E, Budnik B, van Oudenaarden A.

Cell Rep. 2015 Nov 3;13(5):865-73. doi: 10.1016/j.celrep.2015.09.056. Epub 2015 Oct 22.

42.

Design and Analysis of Single-Cell Sequencing Experiments.

Grün D, van Oudenaarden A.

Cell. 2015 Nov 5;163(4):799-810. doi: 10.1016/j.cell.2015.10.039. Review.

43.

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

Soh YQ, Junker JP, Gill ME, Mueller JL, van Oudenaarden A, Page DC.

PLoS Genet. 2015 Sep 17;11(9):e1005531. doi: 10.1371/journal.pgen.1005531. eCollection 2015 Sep.

44.

Genome-wide maps of nuclear lamina interactions in single human cells.

Kind J, Pagie L, de Vries SS, Nahidiazar L, Dey SS, Bienko M, Zhan Y, Lajoie B, de Graaf CA, Amendola M, Fudenberg G, Imakaev M, Mirny LA, Jalink K, Dekker J, van Oudenaarden A, van Steensel B.

Cell. 2015 Sep 24;163(1):134-47. doi: 10.1016/j.cell.2015.08.040. Epub 2015 Sep 10.

45.

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

Grün D, Lyubimova A, Kester L, Wiebrands K, Basak O, Sasaki N, Clevers H, van Oudenaarden A.

Nature. 2015 Sep 10;525(7568):251-5. doi: 10.1038/nature14966. Epub 2015 Aug 19.

PMID:
26287467
46.

DAZL regulates Tet1 translation in murine embryonic stem cells.

Welling M, Chen HH, Muñoz J, Musheev MU, Kester L, Junker JP, Mischerikow N, Arbab M, Kuijk E, Silberstein L, Kharchenko PV, Geens M, Niehrs C, van de Velde H, van Oudenaarden A, Heck AJ, Geijsen N.

EMBO Rep. 2015 Jul;16(7):791-802. doi: 10.15252/embr.201540538. Epub 2015 Jun 15.

47.

Single-cell transcriptomics enters the age of mass production.

Junker JP, van Oudenaarden A.

Mol Cell. 2015 May 21;58(4):563-4. doi: 10.1016/j.molcel.2015.05.019.

48.

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

van Zon JS, Kienle S, Huelsz-Prince G, Barkoulas M, van Oudenaarden A.

Nat Commun. 2015 May 11;6:7053. doi: 10.1038/ncomms8053.

49.

Prospective derivation of a living organoid biobank of colorectal cancer patients.

van de Wetering M, Francies HE, Francis JM, Bounova G, Iorio F, Pronk A, van Houdt W, van Gorp J, Taylor-Weiner A, Kester L, McLaren-Douglas A, Blokker J, Jaksani S, Bartfeld S, Volckman R, van Sluis P, Li VS, Seepo S, Sekhar Pedamallu C, Cibulskis K, Carter SL, McKenna A, Lawrence MS, Lichtenstein L, Stewart C, Koster J, Versteeg R, van Oudenaarden A, Saez-Rodriguez J, Vries RG, Getz G, Wessels L, Stratton MR, McDermott U, Meyerson M, Garnett MJ, Clevers H.

Cell. 2015 May 7;161(4):933-45. doi: 10.1016/j.cell.2015.03.053.

50.

Gene expression. MicroRNA control of protein expression noise.

Schmiedel JM, Klemm SL, Zheng Y, Sahay A, Blüthgen N, Marks DS, van Oudenaarden A.

Science. 2015 Apr 3;348(6230):128-32. doi: 10.1126/science.aaa1738.

Supplemental Content

Loading ...
Support Center