Alexander van Oudenaarden

62.1k citations

200 papers · 36.6k indexed · 25 hit papers · h-index 91

Molecular Biology top 0.02%
Genetics top 0.05%
Cancer Research top 0.1%
Oncology top 0.5%
Biomedical Engineering top 0.5%

Co-authors: Arjun Raj Mukund Thattai Dominic Grün Hans Clevers Lennart Kester Scott A. Rifkin Ertuğrul M. Özbudak Jerome T. Mettetal
Topics: Gene Regulatory Network Analysis (42 papers)Single-cell and spatial transcriptomics (39 papers)Epigenetics and DNA Methylation (21 papers)
Cited by: Aging Biophysics Molecular Biology
Journals: Nature Science Cell
Partner nations: Netherlands United States Germany

In The Last Decade

Alexander van Oudenaarden

193 papers receiving 36.2k citations

Hit Papers

5 papers align trajectories

What are hit papers?

Hit papers significantly outperform the citation benchmark for their cohort. A paper qualifies if it has ≥500 total citations, achieves ≥1.5× the top-1% citation threshold for papers in the same subfield and year (this is the minimum needed to enter the top 1%, not the average within it), or reaches the top citation threshold in at least one of its specific research topics.

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

2009 2.3k citations Ahmad M. Khalil, Mitchell Guttman et al. Proceedings of the National Academy of Sciences profile →
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

2008 1.8k citations Arjun Raj, Alexander van Oudenaarden profile →
Imaging individual mRNA molecules using multiple singly labeled probes

2008 1.5k citations Arjun Raj, Alexander van Oudenaarden et al. profile →
Regulation of noise in the expression of a single gene

2002 1.2k citations Alexander van Oudenaarden et al. profile →
Intrinsic noise in gene regulatory networks

2001 1.1k citations Alexander van Oudenaarden et al. Proceedings of the National Academy of Sciences profile →
Single-cell messenger RNA sequencing reveals rare intestinal cell types

2015 847 citations Anna Lyubimova, Kay Wiebrands et al. Nature profile →
A Single-Cell Transcriptome Atlas of the Human Pancreas

2016 787 citations Mauro J. Muraro, Alexander van Oudenaarden et al. profile →
Multistability in the lactose utilization network of Escherichia coli

2004 761 citations Alexander van Oudenaarden et al. Nature profile →
Slug and Sox9 Cooperatively Determine the Mammary Stem Cell State

2012 755 citations Shalev Itzkovitz, George W. Bell et al. profile →
Direct cell reprogramming is a stochastic process amenable to acceleration

2009 749 citations Bernardo Pando, Alexander van Oudenaarden et al. Nature profile →
Cellular Decision Making and Biological Noise: From Microbes to Mammals

2011 723 citations Alexander van Oudenaarden et al. profile →
Stochastic switching as a survival strategy in fluctuating environments

2008 647 citations Jerome T. Mettetal, Alexander van Oudenaarden et al. profile →
Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

2012 626 citations Sandy Klemm, Alexander van Oudenaarden et al. profile →
Noise Propagation in Gene Networks

2005 615 citations Alexander van Oudenaarden et al. Science profile →
Dll1+ secretory progenitor cells revert to stem cells upon crypt damage

2012 584 citations Johan H. van Es, Marc van de Wetering et al. profile →
MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals

2007 568 citations Alexander van Oudenaarden et al. profile →
The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent ‘+4’ cell markers

2012 562 citations Daniel E. Stange, Marc van de Wetering et al. The EMBO Journal profile →
Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

2016 543 citations Alexander van Oudenaarden et al. profile →
Using Gene Expression Noise to Understand Gene Regulation

2012 539 citations Alexander van Oudenaarden et al. Science profile →
Snowdrift game dynamics and facultative cheating in yeast

2009 500 citations Alexander van Oudenaarden et al. Nature profile →
Validation of noise models for single-cell transcriptomics

2014 477 citations Alexander van Oudenaarden et al. profile →
Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

2016 412 citations Onur Başak, Kay Wiebrands et al. profile →
De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

2016 370 citations Mauro J. Muraro, Kay Wiebrands et al. profile →
Blastocyst-like structures generated solely from stem cells

2018 360 citations Alexander van Oudenaarden et al. Nature profile →
An in vitro model of early anteroposterior organization during human development

2020 302 citations Naomi Moris, Kerim Anlaş et al. Nature profile →

Peers

Countries citing papers authored by Alexander van Oudenaarden

Since Specialization

Citations

This map shows the geographic impact of Alexander van Oudenaarden's research. It shows the number of citations coming from papers published by authors working in each country. You can also color the map by specialization and compare the number of citations received by Alexander van Oudenaarden with the expected number of citations based on a country's size and research output (numbers larger than one mean the country cites Alexander van Oudenaarden more than expected).

Fields of papers citing papers by Alexander van Oudenaarden

Since Specialization

Physical SciencesHealth SciencesLife SciencesSocial Sciences

This network shows the impact of papers produced by Alexander van Oudenaarden. Nodes represent research fields, and links connect fields that are likely to share authors. Colored nodes show fields that tend to cite the papers produced by Alexander van Oudenaarden. The network helps show where Alexander van Oudenaarden may publish in the future.

Co-authorship network of co-authors of Alexander van Oudenaarden

This figure shows the co-authorship network connecting the top 25 collaborators of Alexander van Oudenaarden. A scholar is included among the top collaborators of Alexander van Oudenaarden based on the total number of citations received by their joint publications. Widths of edges represent the number of papers authors have co-authored together. Node borders signify the number of papers an author published with Alexander van Oudenaarden. Alexander van Oudenaarden is excluded from the visualization to improve readability, since they are connected to all nodes in the network.

All Works

Sort: Min cites: Since: Top N: Style:

20 of 20 papers shown

#	Work	Indexed citations
1	RNA transcripts regulate G-quadruplex landscapes through G-loop formation 2025 ·Science ·Koichi Sato,Jing Lyu,Jeroen van den Berg,(unknown),(unknown),Carmen Navarro,Joost Schimmel,Clara Esteban-Jurado,(unknown),(unknown),(unknown),Francesca Mattiroli,Alexander van Oudenaarden,Marcel Tijsterman,Simon J. Elsässer,Puck Knipscheer	2
2	Self-organizing models of human trunk organogenesis recapitulate spinal cord and spine co-morphogenesis 2023 ·Nature Biotechnology ·Simona Gribaudo,(unknown),(unknown),(unknown),Anna Lyubimova,(unknown),Julien Ferent,Xavier Morin,Alexander van Oudenaarden,Stéphane Nedelec	41
3	Embryo‐uterine interaction coordinates mouse embryogenesis during implantation 2023 ·The EMBO Journal ·Vladyslav Bondarenko,Mikhail Nikolaev,(unknown),Roman Belousov,Adrian Wolny,Marloes Blotenburg,Peter Zeller,Saba Rezakhani,(unknown),Virginie Uhlmann,Lars Hufnagel,Anna Kreshuk,Jan Ellenberg,Alexander van Oudenaarden,Anna Erzberger,Matthias P. Lütolf,Takashi Hiiragi	20
4	SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors 2023 ·Nature Communications ·Ning Qing Liu,(unknown),Lars Custers,Peter Zeller,Hans Teunissen,(unknown),(unknown),(unknown),Eelco W. Hoving,Alexander van Oudenaarden,Elzo de Wit,Jarno Drost	14
5	BMP gradient along the intestinal villus axis controls zonated enterocyte and goblet cell states 2022 ·Cell Reports ·Joep Beumer,Jens Puschhof,Fjodor Yousef Yengej,(unknown),Adriana Martínez-Silgado,Marloes Blotenburg,Harry Begthel,Charelle Boot,Alexander van Oudenaarden,Ye‐Guang Chen,Hans Clevers	70
6	An in vitro model of early anteroposterior organization during human developmentbreakdown → 2020 ·Nature ·Naomi Moris,Kerim Anlaş,Susanne van den Brink,Anna Alemany,(unknown),Sabitri Ghimire,Tina Balayo,Alexander van Oudenaarden,Alfonso Martínez Arias	302
7	Spindle checkpoint silencing at kinetochores with submaximal microtubule occupancy 2019 ·Journal of Cell Science ·Banafsheh Etemad,Ábel Vértesy,(unknown),Carlos Sacristán,Alexander van Oudenaarden,Geert J.P.L. Kops	21
8	Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy 2018 ·Proceedings of the National Academy of Sciences ·Onur Başak,Teresa G. Krieger,Mauro J. Muraro,Kay Wiebrands,Daniel E. Stange,(unknown),N.C. Rivron,Marc van de Wetering,Johan H. van Es,Alexander van Oudenaarden,Benjamin D. Simons,Hans Clevers	121
9	Neuromesodermal progenitors are a conserved source of spinal cord with divergent growth dynamics 2018 ·Development ·(unknown),Timothy Fulton,Maria Florescu,Gopi Shah,Leila Mureşan,Martin O. Lenz,(unknown),Jan Huisken,Alexander van Oudenaarden,Benjamin Steventon	51
10	Dynamics of lineage commitment revealed by single-cell transcriptomics of differentiating embryonic stem cells 2017 ·Nature ·Stefan Semrau,Johanna Goldmann,Magali Soumillon,Tarjei S. Mikkelsen,Alexander van Oudenaarden,Rudolf Jaenisch	4
11	Reg4 ⁺ deep crypt secretory cells function as epithelial niche for Lgr5 ⁺ stem cells in colon 2016 ·Proceedings of the National Academy of Sciences ·Nobuo Sasaki,Norman Sachs,Kay Wiebrands,Saskia I. J. Ellenbroek,Arianna Fumagalli,Anna Lyubimova,Harry Begthel,Maaike van den Born,Johan H. van Es,Wouter R. Karthaus,Vivian Li,Carmen López‐Iglesias,Peter J. Peters,Jacco van Rheenen,Alexander van Oudenaarden,Hans Clevers	206
12	MicroRNA control of protein expression noise 2015 ·Science ·Jörn M. Schmiedel,Sandy Klemm,Yannan Zheng,(unknown),Nils Blüthgen,Debora S. Marks,Alexander van Oudenaarden	281
13	Genetic and Phenotypic Diversity in Breast Tumor Metastases 2014 ·Cancer Research ·Vanessa Almendro,Hee Jung Kim,Yu-Kang Cheng,Mithat Gönen,Shalev Itzkovitz,Pedram Argani,Alexander van Oudenaarden,Saraswati Sukumar,Franziska Michor,Kornélia Polyák	129
14	Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins 2013 ·Proceedings of the National Academy of Sciences ·Lenny Teytelman,Deborah Thurtle-Schmidt,Jasper Rine,Alexander van Oudenaarden	290
15	Caenorhabditis elegans aristaless/Arx gene alr-1 restricts variable gene expression 2011 ·Proceedings of the National Academy of Sciences ·Irini Topalidou,Alexander van Oudenaarden,Martin Chalfie	38
16	Genes methylated by DNA methyltransferase 3b are similar in mouse intestine and human colon cancer 2011 ·Journal of Clinical Investigation ·Eveline J. Steine,Mathias Ehrich,George W. Bell,Arjun Raj,(unknown),Alexander van Oudenaarden,Rudolf Jaenisch,Heinz Linhart	55
17	Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expressionbreakdown → 2009 ·Proceedings of the National Academy of Sciences ·Ahmad M. Khalil,Mitchell Guttman,Maite Huarte,Manuel Garber,Arjun Raj,(unknown),(unknown),(unknown),B Bernstein,Alexander van Oudenaarden,Aviv Regev,Eric S. Lander,John L. Rinn	2331
18	Circadian Gating of the Cell Cycle Revealed in Single Cyanobacterial Cells 2009 ·DSpace@MIT (Massachusetts Institute of Technology) ·Bernardo Pando,Guogang Dong,Susan S. Golden,Alexander van Oudenaarden,Qiong Yang	129
19	Cellular asymmetry and individuality in directional sensing 2006 ·Proceedings of the National Academy of Sciences ·Azadeh Samadani,Jerome T. Mettetal,Alexander van Oudenaarden	63
20	Quantum vortices and quantum interference effects in circuits of small tunnel junctions 1998 ·Research Repository (Delft University of Technology) ·Alexander van Oudenaarden	0

About Alexander van Oudenaarden

Alexander van Oudenaarden is a scholar working on Aging, Molecular Biology and Biophysics, having authored 200 papers that have together received 36.6k indexed citations. Recurring topics across this work include Gene Regulatory Network Analysis (42 papers), Single-cell and spatial transcriptomics (39 papers) and Epigenetics and DNA Methylation (21 papers). The work is most often cited by research in Aging (1.2k citations), Biophysics (2.6k citations) and Molecular Biology (29.2k citations). Alexander van Oudenaarden has collaborated with scholars based in Netherlands, United States and Germany. Frequent co-authors include Arjun Raj, Mukund Thattai, Dominic Grün, Hans Clevers, Lennart Kester, Scott A. Rifkin, Ertuğrul M. Özbudak, Jerome T. Mettetal, Murat Açar and Juan Manuel Pedraza. Their work appears in journals such as Nature, Science and Cell.

Rankless uses publication and citation data sourced from OpenAlex, an open and comprehensive bibliographic database. While OpenAlex provides broad and valuable coverage of the global research landscape, it—like all bibliographic datasets—has inherent limitations. These include incomplete records, variations in author disambiguation, differences in journal indexing, and delays in data updates. As a result, some metrics and network relationships displayed in Rankless may not fully capture the entirety of a scholar's output or impact.

Explore authors with similar magnitude of impact