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2018

Determinants of promoter and enhancer transcription directionality in metazoans.
Ibrahim, M.M. and Karabacak, A. and Glahs, A. and Kolundzic, E. and Hirsekorn, A. and Carda, A. and Tursun, B. and Zinzen, R.P. and Lacadie, S.A. and Ohler, U.
Nature Communications 9 (1): 4472. 26 October 2018

Editorial overview.
Shvartsman, S. and Zinzen, R.
Current Opinion in Systems Biology 11 : v. October 2018

High-throughput identification of RNA nuclear enrichment sequences.
Shukla, C.J. and McCorkindale, A.L. and Gerhardinger, C. and Korthauer, K.D. and Cabili, M.N. and Shechner, D.M. and Irizarry, R.A. and Maass, P. and Rinn, J.L.
EMBO Journal 37 : e98452. 15 March 2018

2017

Determinants of transcription initiation directionality in metazoans.
Ibrahim, M.M. and Karabacak, A. and Glahs, A. and Kolundzic, E. and Hirsekorn, A. and Carda, A. and Tursun, B. and Zinzen, R.P. and Lacadie, S.A. and Ohler, U.
bioRxiv : 224642. 24 November 2017

McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.
Hafez, D. and Karabacak, A. and Krueger, S. and Hwang, Y.C. and Wang, L.S. and Zinzen, R.P. and Ohler, U.
Genome Biology 18 (1): 199. 26 October 2017

The Drosophila embryo at single-cell transcriptome resolution.
Karaiskos, N. and Wahle, P. and Alles, J. and Boltengagen, A. and Ayoub, S. and Kipar, C. and Kocks, C. and Rajewsky, N. and Zinzen, R.P.
Science 358 (6360): 194-199. 13 October 2017

Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J. and Karaiskos, N. and Praktiknjo, S.D. and Grosswendt, S. and Wahle, P. and Ruffault, P.L. and Ayoub, S. and Schreyer, L. and Boltengagen, A. and Birchmeier, C. and Zinzen, R. and Kocks, C. and Rajewsky, N.
BMC Biology 15 (1): 44. 19 May 2017

Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J. and Karaiskos, N. and Praktiknjo, S. and Grosswendt, S. and Wahle, P. and Ruffault, P.L. and Ayoub, S. and Schreyer, L. and Boltengagen, A. and Birchmeier, C. and Zinzen, R. and Kocks, C. and Rajewsky, N.
bioRxiv : 099473. 13 April 2017

The Drosophila embryo at single cell transcriptome resolution.
Karaiskos, N. and Wahle, P. and Alles, J. and Boltengagen, A. and Ayoub, S. and Kipar, C. and Kocks, C. and Rajewsky, N. and Zinzen, R.P.
bioRxiv : 117382. 17 March 2017

2016

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.
Cheng, Z. and Teo, G. and Krueger, S. and Rock, T.M. and Koh, H.W.L. and Choi, H. and Vogel, C.
Molecular Systems Biology 12 (1): 855. 20 January 2016

Putting chromatin in its place: the pioneer factor NeuroD1 modulates chromatin state to drive cell fate decisions.
Glahs, A. and Zinzen, R.P.
EMBO Journal 35 (1): 1-3. 4 January 2016

2015

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.
Cheng, Z. and Teo, G. and Krueger, S. and Rock, T. and Koh, H.W.L. and Choi, H. and Vogel, C.
bioRxiv : 032797. 26 November 2015

miR-184 regulates pancreatic β-cell function according to glucose metabolism.
Tattikota, S.G. and Rathjen, T. and Hausser, J. and Khedkar, A. and Kabra, U.D. and Pandey, V.K. and Sury, M.D. and Wessels, H.H. and Mollet, I.G. and Eliasson, L. and Selbach, M. and Zinzen, R.P. and Zavolan, M. and Kadener, S. and Tschöp, M. and Jastroch, M. and Friedländer, M.R. and Poy, M.N.
Journal of Biological Chemistry 290 (33): 20284-20294. 14 August 2015

2014

A conserved role for Snail as a potentiator of active transcription.
Rembold, M. and Ciglar, L. and Yáñez-Cuna, J.O. and Zinzen, R.P. and Girardot, C. and Jain, A. and Welte, M.A. and Stark, A. and Leptin, M. and Furlong, E.E.M.
Genes & Development 28 (2): 167-181. 15 January 2014

2012

Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
Bonn, S. and Zinzen, R.P. and Perez-Gonzalez, A. and Riddell, A. and Gavin, A.C. and Furlong, E.E.
Nature Protocols 7 (5): 978-994. May 2012

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development.
Bonn, S. and Zinzen, R.P. and Girardot, C. and Gustafson, E.H. and Perez-Gonzalez, A. and Delhomme, N. and Ghavi-Helm, Y. and Wilczynski, B. and Riddell, A. and Furlong, E.E.
Nature Genetics 44 (2): 148-156. February 2012

2009

Combinatorial binding predicts spatio-temporal cis-regulatory activity.
Zinzen, R.P. and Girardot, C. and Gagneur, J. and Braun, M. and Furlong, E.E.
Nature 462 (7269): 65-70. 5 November 2009

2008

Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.
Zinzen, R.P. and Furlong, E.E.
Genome Biology 9 (11): 240. 4 November 2008

2007

Evolution of the dorsal-ventral patterning network in the mosquito, Anopheles gambiae.
Goltsev, Y. and Fuse, N. and Frasch, M. and Zinzen, R.P. and Lanzaro, G. and Levine, M.
Development 134 (13): 2415-2424. July 2007

Enhancer responses to similarly distributed antagonistic gradients in development.
Zinzen, R.P. and Papatsenko, D.
PLoS Computational Biology 3 (5): e84. 11 May 2007

Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo.
Zeitlinger, J. and Zinzen, R.P. and Stark, A. and Kellis, M. and Zhang, H. and Young, R.A. and Levine, M.
Genes & Development 21 (4): 385-390. 15 February 2007

2006

Evolution of the ventral midline in insect embryos.
Zinzen, R.P. and Cande, J. and Ronshaugen, M. and Papatsenko, D. and Levine, M.
Developmental Cell 11 (6): 895-902. December 2006

Computational models for neurogenic gene expression in the Drosophila embryo.
Zinzen, R.P. and Senger, K. and Levine, M. and Papatsenko, D.
Current Biology 16 (13): 1358-1365. 11 July 2006

Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway.
De Renzis, S. and Yu, J. and Zinzen, R.P. and Wieschaus, E.
Developmental Cell 10 (2): 257-264. February 2006

2005

Spatial regulation of microRNA gene expression in the Drosophila embryo.
Biemar, F. and Zinzen, R.P. and Ronshaugen, M. and Sementchenko, V. and Manak, J.R. and Levine, M.S.
Proceedings of the National Academy of Sciences of the United States of America 102 (44): 15907-15911. 1 November 2005

2004

A regulatory code for neurogenic gene expression in the Drosophila embryo.
Markstein, M. and Zinzen, R.P. and Markstein, P. and Yee, K.P. and Erives, A. and Stathopoulos, A. and Levine, M.
Development 131 (10): 2387-2394. May 2004

Template requirements for telomerase translocation in Kluyveromyces lactis.
Underwood, D.H. and Zinzen, R.P. and McEachern, M.J.
Molecular and Cellular Biology 24 (2): 912-923. January 2004

This list was generated on Wed Nov 14 02:18:53 2018 CET.
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