Publications

2018

Pavel Vopalensky, Sabrina Pralow and Nadine L Vastenhouw
Reduced expression of the Nodal coreceptor Oep causes loss of mesendodermal competence in zebrafish
Accepted for publication in Development
 
Stapel LC, Broaddus C, Vastenhouw NL
Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos
Methods Mol Biol 1649:143-162 (2018)

2017

Lennart Hilbert, Yuko Sato, Hiroshi Kimura, Frank Jülicher, Alf Honigmann, Vasily Zaburdaev, and Nadine Vastenhouw
Transcription establishes microenvironments that organize euchromatin
Posted on the bioRxiv on Dec 15 2017
 
Kumar M, Joseph SR, Augsburg M, Bogdanova A, Drechsel D, Vastenhouw NL, Buchholz F, Gentzel M, Shevchenko A.
MS Western, a method of multiplexed absolute protein quantification is a practical alternative to Western blotting
Mol Cell Proteomics (2017 Nov 30) [Epub ahead of print] 
 
Stapel, L Carine; Zechner, Christoph; Vastenhouw, Nadine L
Uniform gene expression in embryos is achieved by temporal averaging of transcription noise
Genes Dev 31: 1635-1640 (2017)
 
Boothe, Tobias; Hilbert, Lennart; Heide, Michael; Berninger, Lea; Hüttner, Wieland B ; Zaburdaev, Vasily; Vastenhouw, Nadine; Myers, Eugene W; Drechsel, David N; Rink, Jochen C
A tunable refractive index matching medium for live imaging cells, tissues and model organisms
eLife, 27240 2017
 
Joseph, Shai R; Pálfy, Máté; Hilbert, Lennart; Kumar, Mukesh; Karschau, Jens; Zaburdaev, Vasily; Shevchenko, Andrej; Vastenhouw, Nadine L
Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos
eLife, 23326 (2017)
 
Palfy, Máté; Joseph, Shai R; Vastenhouw, Nadine L
The timing of zygotic genome activation
Current Opinion in Genetics and Development, 43, pp. 53-60 (2017)

2016

Stapel, L Carine; Lombardot, Benoit; Broaddus, Coleman; Kainmueller, Dagmar; Jug, Florian; Myers, Eugene W.; Vastenhouw, Nadine L.
Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos
Development, 143, no. 3, pp. 540-546 (2016)

2014

Stapel, L Carine; Vastenhouw, Nadine
Message control in developmental transitions; deciphering chromatin's role using zebrafish genomics.
Brief Funct Genomics, 13, no. 2, pp. 106-120 (2014)
Pubmed Entry

Zhang, Yang; Vastenhouw, Nadine; Feng, Jianxing; Fu, Kai; Wang, Chenfei; Ge, Ying; Hummelen, Paul van; Schier, Alexander F; Liu, Xiaole Shirley
Canonical nucleosome organization at promoters forms during genome activation.
Genome Res, 24, no. 2, pp. 260-266 (2014)
Pubmed Entry, Download PDF

2012

Vastenhouw, Nadine; Schier, Alexander F
Bivalent histone modifications in early embryogenesis.
Curr Opin Cell Biol, 24, no. 3, pp. 374-386 (2012)
Pubmed Entry, Download PDF

Pauli, Andrea; Valen, Eivind; Lin, Michael F; Garber, Manuel; Vastenhouw, Nadine; Levin, Joshua Z; Fan, Lin; Sandelin, Albin; Rinn, John L; Regev, Aviv; Schier, Alexander F
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
Genome Res, 22, no. 3, pp. 577-591 (2012)
Pubmed Entry

2010

Vastenhouw, Nadine; Zhang, Yang; Woods, Ian G; Imam, Farhad; Regev, Aviv; Liu, X Shirley; Rinn, John L; Schier, Alexander F
Chromatin signature of embryonic pluripotency is established during genome activation.
Nature, 464, no. 7290, pp. 922-926 (2010)
Pubmed Entry

2006

Vastenhouw, Nadine; Brunschwig, Karin; Okihara, Kristy L; Müller, Fritz; Tijsterman, Marcel; Plasterk, Ronald H A
Gene expression: long-term gene silencing by RNAi.
Nature, 442, no. 7105, pp. 882-882 (2006)
Pubmed Entry

2004

Haaften, Gijs van; Vastenhouw, Nadine; Nollen, Ellen A A; Plasterk, Ronald H A; Tijsterman, Marcel
Gene interactions in the DNA damage-response pathway identified by genome-wide RNA-interference analysis of synthetic lethality.
Proc Natl Acad Sci U.S.A., 101, no. 35, pp. 12992-12996 (2004)
Pubmed Entry

Vastenhouw, Nadine; Plasterk, Ronald H A
RNAi protects the Caenorhabditis elegans germline against transposition.
Trends Genet., 20, no. 7, pp. 314-319 (2004)
Pubmed Entry

Robert, V J P; Vastenhouw, Nadine; Plasterk, Ronald H A
RNA interference, transposon silencing, and cosuppression in the Caenorhabditis elegans germ line: similarities and differences.
Cold Spring Harb Symp Quant Biol, 69, pp. 397-402 (2004)
Pubmed Entry

2003

Vastenhouw, Nadine; Fischer, Steffi; Robert, V J P; Thijssen, Karen L; Fraser, Andrew G; Kamath, Ravi S; Ahringer, Julie; Plasterk, Ronald H A
A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans.
Curr Biol, 13, no. 15, pp. 1311-1316 (2003)
Pubmed Entry

2001

Masselink, H; Vastenhouw, Nadine; Bernards, René
B-myb rescues ras-induced premature senescence, which requires its transactivation domain.
Cancer Lett, 171, no. 1, pp. 87-101 (2001)
Pubmed Entry

Berkhout, B; Vastenhouw, Nadine; Klasens, B I; Huthoff, H
Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription.
RNA, 7, no. 8, pp. 1097-1114 (2001)
Pubmed Entry

2017

Stapel LC, Broaddus C, Vastenhouw NL
Detection and Automated Analysis of Single Transcripts at Subcellular Resolution in Zebrafish Embryos
Methods Mol Biol 1649:143-162 (2018)
 
Stapel, L Carine; Zechner, Christoph; Vastenhouw, Nadine L
Uniform gene expression in embryos is achieved by temporal averaging of transcription noise
Genes Dev 31: 1635-1640 (2017)
 
Boothe, Tobias; Hilbert, Lennart; Heide, Michael; Berninger, Lea; Hüttner, Wieland B ; Zaburdaev, Vasily; Vastenhouw, Nadine; Myers, Eugene W; Drechsel, David N; Rink, Jochen C
A tunable refractive index matching medium for live imaging cells, tissues and model organisms
eLife, 27240 2017
 
Joseph, Shai R; Pálfy, Máté; Hilbert, Lennart; Kumar, Mukesh; Karschau, Jens; Zaburdaev, Vasily; Shevchenko, Andrej; Vastenhouw, Nadine L
Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos
eLife, 23326 (2017)
 
Palfy, Máté; Joseph, Shai R; Vastenhouw, Nadine L
The timing of zygotic genome activation
Current Opinion in Genetics and Development, 43, pp. 53-60 (2017)

2016

Stapel, L Carine; Lombardot, Benoit; Broaddus, Coleman; Kainmueller, Dagmar; Jug, Florian; Myers, Eugene W.; Vastenhouw, Nadine L.
Automated detection and quantification of single RNAs at cellular resolution in zebrafish embryos
Development, 143, no. 3, pp. 540-546 (2016)

2014

Stapel, L Carine; Vastenhouw, Nadine
Message control in developmental transitions; deciphering chromatin's role using zebrafish genomics.
Brief Funct Genomics, 13, no. 2, pp. 106-120 (2014)
Pubmed Entry

Zhang, Yang; Vastenhouw, Nadine; Feng, Jianxing; Fu, Kai; Wang, Chenfei; Ge, Ying; Hummelen, Paul van; Schier, Alexander F; Liu, Xiaole Shirley
Canonical nucleosome organization at promoters forms during genome activation.
Genome Res, 24, no. 2, pp. 260-266 (2014)
Pubmed Entry, Download PDF

2012

Vastenhouw, Nadine; Schier, Alexander F
Bivalent histone modifications in early embryogenesis.
Curr Opin Cell Biol, 24, no. 3, pp. 374-386 (2012)
Pubmed Entry, Download PDF

Pauli, Andrea; Valen, Eivind; Lin, Michael F; Garber, Manuel; Vastenhouw, Nadine; Levin, Joshua Z; Fan, Lin; Sandelin, Albin; Rinn, John L; Regev, Aviv; Schier, Alexander F
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.
Genome Res, 22, no. 3, pp. 577-591 (2012)
Pubmed Entry

2010

Vastenhouw, Nadine; Zhang, Yang; Woods, Ian G; Imam, Farhad; Regev, Aviv; Liu, X Shirley; Rinn, John L; Schier, Alexander F
Chromatin signature of embryonic pluripotency is established during genome activation.
Nature, 464, no. 7290, pp. 922-926 (2010)
Pubmed Entry

2006

Vastenhouw, Nadine; Brunschwig, Karin; Okihara, Kristy L; Müller, Fritz; Tijsterman, Marcel; Plasterk, Ronald H A
Gene expression: long-term gene silencing by RNAi.
Nature, 442, no. 7105, pp. 882-882 (2006)
Pubmed Entry

2004

Haaften, Gijs van; Vastenhouw, Nadine; Nollen, Ellen A A; Plasterk, Ronald H A; Tijsterman, Marcel
Gene interactions in the DNA damage-response pathway identified by genome-wide RNA-interference analysis of synthetic lethality.
Proc Natl Acad Sci U.S.A., 101, no. 35, pp. 12992-12996 (2004)
Pubmed Entry

Vastenhouw, Nadine; Plasterk, Ronald H A
RNAi protects the Caenorhabditis elegans germline against transposition.
Trends Genet., 20, no. 7, pp. 314-319 (2004)
Pubmed Entry

Robert, V J P; Vastenhouw, Nadine; Plasterk, Ronald H A
RNA interference, transposon silencing, and cosuppression in the Caenorhabditis elegans germ line: similarities and differences.
Cold Spring Harb Symp Quant Biol, 69, pp. 397-402 (2004)
Pubmed Entry

2003

Vastenhouw, Nadine; Fischer, Steffi; Robert, V J P; Thijssen, Karen L; Fraser, Andrew G; Kamath, Ravi S; Ahringer, Julie; Plasterk, Ronald H A
A genome-wide screen identifies 27 genes involved in transposon silencing in C. elegans.
Curr Biol, 13, no. 15, pp. 1311-1316 (2003)
Pubmed Entry

2001

Masselink, H; Vastenhouw, Nadine; Bernards, René
B-myb rescues ras-induced premature senescence, which requires its transactivation domain.
Cancer Lett, 171, no. 1, pp. 87-101 (2001)
Pubmed Entry

Berkhout, B; Vastenhouw, Nadine; Klasens, B I; Huthoff, H
Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription.
RNA, 7, no. 8, pp. 1097-1114 (2001)
Pubmed Entry