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1

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

Jaitin, Diego Adhemar, Weiner, Assaf, Yofe, Ido, Lara-Astiaso, David, Keren-Shaul, Hadas, David, Eyal, Salame, Tomer Meir, Tanay, Amos, van Oudenaarden, Alexander, Amit, Ido

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 9.21 MB

english, 2016

2

Blastocyst-like structures generated solely from stem cells

Rivron, Nicolas C., Frias-Aldeguer, Javier, Vrij, Erik J., Boisset, Jean-Charles, Korving, Jeroen, Vivié, Judith, Truckenmüller, Roman K., van Oudenaarden, Alexander, van Blitterswijk, Clemens A., Gei

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 22.15 MB

english, 2018

3

Cellular Decision Making and Biological Noise: From Microbes to Mammals

Gábor Balázsi, Alexander van Oudenaarden, James J. Collins

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2011

4

MicroRNA-Mediated Feedback and Feedforward Loops Are Recurrent Network Motifs in Mammals

John Tsang, Jun Zhu, Alexander van Oudenaarden

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 1.86 MB

english, 2007

5

Single-cell messenger RNA sequencing reveals rare intestinal cell types

Grün, Dominic, Lyubimova, Anna, Kester, Lennart, Wiebrands, Kay, Basak, Onur, Sasaki, Nobuo, Clevers, Hans, van Oudenaarden, Alexander

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 5.17 MB

english, 2015

6

Design and Analysis of Single-Cell Sequencing Experiments

Grün, Dominic, van Oudenaarden, Alexander

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 1.70 MB

english, 2015

7

Contributions of low molecule number and chromosomal positioning to stochastic gene expression

Becskei, Attila, Kaufmann, Benjamin B, van Oudenaarden, Alexander

Journal:

Nature Genetics

Année:

2005

Langue:

english

Fichier:

PDF, 431 KB

english, 2005

8

Synthetic biology: understanding biological design from synthetic circuits

Mukherji, Shankar, van Oudenaarden, Alexander

Journal:

Nature Reviews Genetics

Année:

2009

Langue:

english

Fichier:

PDF, 525 KB

english, 2009

9

Single-Molecule Approaches to Stochastic Gene Expression

Raj, Arjun, van Oudenaarden, Alexander

Journal:

Annual Review of Biophysics

Année:

2009

Langue:

english

Fichier:

PDF, 399 KB

english, 2009

10

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

Arjun Raj, Alexander van Oudenaarden

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2008

11

Nature, nurture, or just blind chance: Stochastic gene expression and its consequences

van Oudenaarden, Alexander

Journal:

Biophysical Journal

Année:

2009

Langue:

english

Fichier:

PDF, 34 KB

english, 2009

12

Feedback Control of Gene Expression Variability in the Caenorhabditis elegans Wnt Pathway

Ji, Ni, Middelkoop, Teije C., Mentink, Remco A., Betist, Marco C., Tonegawa, Satto, Mooijman, Dylan, Korswagen, Hendrik C., van Oudenaarden, Alexander

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 2.85 MB

english, 2013

13

Every Cell Is Special: Genome-wide Studies Add a New Dimension to Single-Cell Biology

Junker, Jan Philipp, van Oudenaarden, Alexander

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 525 KB

english, 2014

14

Validation of noise models for single-cell transcriptomics

Grün, Dominic, Kester, Lennart, van Oudenaarden, Alexander

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 896 KB

english, 2014

15

Genome-wide RNA Tomography in the Zebrafish Embryo

Junker, Jan Philipp, Noël, Emily S., Guryev, Victor, Peterson, Kevin A., Shah, Gopi, Huisken, Jan, McMahon, Andrew P., Berezikov, Eugene, Bakkers, Jeroen, van Oudenaarden, Alexander

Journal:

Année:

2014

Langue:

english

Fichier:

PDF, 3.81 MB

english, 2014

16

Integrated genome and transcriptome sequencing of the same cell

Dey, Siddharth S, Kester, Lennart, Spanjaard, Bastiaan, Bienko, Magda, van Oudenaarden, Alexander

Journal:

Nature Biotechnology

Année:

2015

Langue:

english

Fichier:

PDF, 810 KB

english, 2015

17

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

Mooijman, Dylan, Dey, Siddharth S, Boisset, Jean-Charles, Crosetto, Nicola, van Oudenaarden, Alexander

Journal:

Nature Biotechnology

Année:

2016

Langue:

english

Fichier:

PDF, 1.27 MB

english, 2016

18

Identity and dynamics of mammary stem cells during branching morphogenesis

Scheele, Colinda L. G. J., Hannezo, Edouard, Muraro, Mauro J., Zomer, Anoek, Langedijk, Nathalia S. M., van Oudenaarden, Alexander, Simons, Benjamin D., van Rheenen, Jacco

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 16.44 MB

english, 2017

19

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, Christoph G., Droste, Rita, van Oudenaarden, Alexander, Horvitz, H. Robert, Ahringer, Julie

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 16.33 MB

english, 2018

20

Spindle checkpoint silencing at kinetochores with submaximal microtubule occupancy

Etemad, Banafsheh, Vertesy, Abel, Kuijt, Timo E. F., Sacristan, Carlos, van Oudenaarden, Alexander, Kops, Geert J. P. L.

Journal:

Journal of Cell Science

Année:

2019

Langue:

english

Fichier:

PDF, 13.94 MB

english, 2019

21

Spindle checkpoint silencing at kinetochores with submaximal microtubule occupancy

Etemad, Banafsheh, Vertesy, Abel, Kuijt, Timo E. F., Sacristan, Carlos, van Oudenaarden, Alexander, Kops, Geert J. P. L.

Journal:

Journal of Cell Science

Année:

2019

Fichier:

PDF, 13.94 MB

2019

22

Cell Type Purification by Single-Cell Transcriptome-Trained Sorting

Baron, Chloé S., Barve, Aditya, Muraro, Mauro J., van der Linden, Reinier, Dharmadhikari, Gitanjali, Lyubimova, Anna, de Koning, Eelco J.P., van Oudenaarden, Alexander

Journal:

Année:

2019

Langue:

english

Fichier:

PDF, 15.24 MB

english, 2019

23

10.1038/35808

van Oudenaarden, Alexander, Devoret, Michel H., Nazarov, Yu. V., Mooij, J. E.

Journal:

Année:

1998

Langue:

english

Fichier:

PDF, 246 KB

english, 1998

24

10.1038/358116a0

van Oudenaarden, Alexander, Devoret, Michel H., Nazarov, Yu. V., Mooij, J. E.

Journal:

Année:

1992

Fichier:

PDF, 172 KB

1992

25

10.1038/358115b0

van Oudenaarden, Alexander, Devoret, Michel H., Nazarov, Yu. V., Mooij, J. E.

Journal:

Année:

1992

Fichier:

PDF, 194 KB

1992

26

Synthetic biology: The yin and yang of nature

Gore, Jeff, van Oudenaarden, Alexander

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 844 KB

english, 2009

27

Microbiology: Altruistic defence

Youk, Hyun, van Oudenaarden, Alexander

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 231 KB

english, 2010

28

10.1038/70281

van Oudenaarden, Alexander, Theriot, Julie A.

Journal:

Nature Cell Biology

Année:

1999

Langue:

english

Fichier:

PDF, 563 KB

english, 1999

29

Multistability in the lactose utilization network of Escherichia coli

Ozbudak, Ertugrul M., Thattai, Mukund, Lim, Han N., Shraiman, Boris I., van Oudenaarden, Alexander

Journal:

Année:

2004

Langue:

english

Fichier:

PDF, 823 KB

english, 2004

30

Enhancement of cellular memory by reducing stochastic transitions

Acar, Murat, Becskei, Attila, van Oudenaarden, Alexander

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 296 KB

english, 2005

31

Stochastic gene expression out-of-steady-state in the cyanobacterial circadian clock

Chabot, Jeffrey R., Pedraza, Juan M., Luitel, Prashant, van Oudenaarden, Alexander

Journal:

Année:

2007

Langue:

english

Fichier:

PDF, 689 KB

english, 2007

32

Snowdrift game dynamics and facultative cheating in yeast

Youk, Hyun, van Oudenaarden, Alexander, Gore, Jeff

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 288 KB

english, 2009

33

Direct cell reprogramming is a stochastic process amenable to acceleration

Hanna, Jacob, Saha, Krishanu, Pando, Bernardo, van Zon, Jeroen, Lengner, Christopher J., Creyghton, Menno P., van Oudenaarden, Alexander, Jaenisch, Rudolf

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 681 KB

english, 2009

34

Growth landscape formed by perception and import of glucose in yeast

Youk, Hyun, van Oudenaarden, Alexander

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 459 KB

english, 2009

35

Variability in gene expression underlies incomplete penetrance

Raj, Arjun, Rifkin, Scott A., Andersen, Erik, van Oudenaarden, Alexander

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2010

36

Amplitude control of cell-cycle waves by nuclear import

Becskei, Attila, Boselli, Monica G., Oudenaarden, Alexander van

Journal:

Nature Cell Biology

Année:

2004

Langue:

english

Fichier:

PDF, 1.02 MB

english, 2004

37

Stochastic switching as a survival strategy in fluctuating environments

Acar, Murat, Mettetal, Jerome T, van Oudenaarden, Alexander

Journal:

Nature Genetics

Année:

2008

Langue:

english

Fichier:

PDF, 359 KB

english, 2008

38

A multistep epigenetic switch enables the stable inheritance of DNA methylation states

Lim, Han N, van Oudenaarden, Alexander

Journal:

Nature Genetics

Année:

2007

Langue:

english

Fichier:

PDF, 399 KB

english, 2007

39

Regulation of noise in the expression of a single gene

Ozbudak, Ertugrul M., Thattai, Mukund, Kurtser, Iren, Grossman, Alan D., van Oudenaarden, Alexander

Journal:

Nature Genetics

Année:

2002

Langue:

english

Fichier:

PDF, 159 KB

english, 2002

40

Imaging individual mRNA molecules using multiple singly labeled probes

Raj, Arjun, van den Bogaard, Patrick, Rifkin, Scott A, van Oudenaarden, Alexander, Tyagi, Sanjay

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 331 KB

english, 2008

41

Validating transcripts with probes and imaging technology

Itzkovitz, Shalev, van Oudenaarden, Alexander

Journal:

Année:

2011

Langue:

english

Fichier:

PDF, 594 KB

english, 2011

42

Quantitative Time-Lapse Fluorescence Microscopy in Single Cells

Muzzey, Dale, van Oudenaarden, Alexander

Journal:

Annual Review of Cell and Developmental Biology

Année:

2009

Langue:

english

Fichier:

PDF, 2.71 MB

english, 2009

43

Bloch vortices in one-dimensional Josephson junction arrays

Alexander van Oudenaarden, S. J. K. Várdy, J. E. Mooij

Journal:

Czechoslovak Journal of Physics

Année:

1996

Langue:

english

Fichier:

PDF, 167 KB

english, 1996

44

Biomimetic Systems for Studying Actin-Based Motility

Arpita Upadhyaya, Alexander van Oudenaarden

Journal:

Current Biology

Année:

2003

Langue:

english

Fichier:

PDF, 283 KB

english, 2003

45

Actin Polymerization: Forcing Flat Faces Forward

Arpita Upadhyaya, Alexander van Oudenaarden

Journal:

Current Biology

Année:

2004

Langue:

english

Fichier:

PDF, 110 KB

english, 2004

46

The thrombospondin repeat containing protein MIG-21 controls a left–right asymmetric Wnt signaling response in migrating C. elegans neuroblasts

Teije C. Middelkoop, Lisa Williams, Pei-Tzu Yang, Jeroen Luchtenberg, Marco C. Betist, Ni Ji, Alexander van Oudenaarden, Cynthia Kenyon, Hendrik C. Korswagen

Journal:

Developmental Biology

Année:

2012

Langue:

english

Fichier:

PDF, 1.52 MB

english, 2012

47

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

Yosef Buganim, Dina A. Faddah, Albert W. Cheng, Elena Itskovich, Styliani Markoulaki, Kibibi Ganz, Sandy L. Klemm, Alexander van Oudenaarden, Rudolf Jaenisch

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 55 KB

english, 2012

48

When It Comes to Decisions, Myeloid Progenitors Crave Positive Feedback

Dale Muzzey, Alexander van Oudenaarden

Journal:

Année:

2006

Langue:

english

Fichier:

PDF, 299 KB

english, 2006

49

A Systems-Level Analysis of Perfect Adaptation in Yeast Osmoregulation

Dale Muzzey, Carlos A. Gómez-Uribe, Jerome T. Mettetal, Alexander van Oudenaarden

Journal:

Année:

2009

Langue:

english

Fichier:

PDF, 2.18 MB

english, 2009

50

Elevated ATPase Activity of KaiC Applies a Circadian Checkpoint on Cell Division in Synechococcus elongatus

Guogang Dong, Qiong Yang, Qiang Wang, Yong-Ick Kim, Thammajun L. Wood, Katherine W. Osteryoung, Alexander van Oudenaarden, Susan S. Golden

Journal:

Année:

2010

Langue:

english

Fichier:

PDF, 961 KB

english, 2010