Hafez D.; Karabacak A.; Krueger S.; Hwang Y.C.; Wang L.S.; Zinzen R.P.; Ohler U.
McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes
Genome Biology 18 (1): 199 (2017-10-26)

Karaiskos N.; Wahle P.; Alles J.; Boltengagen A.; Ayoub S.; Kipar C.; Kocks C.; Rajewsky N.; Zinzen R.P.
The Drosophila embryo at single-cell transcriptome resolution
Science 358 (6360): 194-199 (2017-10-13)

Alles J.; Karaiskos N.; Praktiknjo S.D.; Grosswendt S.; Wahle P.; Ruffault P.L.; Ayoub S.; Schreyer L.; Boltengagen A.; Birchmeier C.; Zinzen R.; Kocks C.; Rajewsky N.
Cell fixation and preservation for droplet-based single-cell transcriptomics
BMC Biology 15 (1): 44 (2017-05-19)


Cheng Z.; Teo G.; Krueger S.; Rock T.M.; Koh H.W.L.; Choi H.; Vogel C.
Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress
Molecular Systems Biology 12 (1): 855 (2016-01-20)

Glahs A.; Zinzen R.P.
Putting chromatin in its place: the pioneer factor NeuroD1 modulates chromatin state to drive cell fate decisions
EMBO Journal 35 (1): 1-3 (2016-01-04)


Tattikota S.G.; Rathjen T.; Hausser J.; Khedkar A.; Kabra U.D.; Pandey V.K.; Sury M.D.; Wessels H.H.; Mollet I.G.; Eliasson L.; Selbach M.; Zinzen R.P.; Zavolan M.; Kadener S.; Tschoep M.; Jastroch M.; Friedlaender M.R.; Poy M.N.
miR-184 regulates pancreatic {beta}-cell function according to glucose metabolism
Journal of Biological Chemistry 290 (33): 20284-20294 (2015-08-14)


Rembold M.; Ciglar L.; Yanez-Cuna J.O.; Zinzen R.P.; Girardot C.; Jain A.; Welte M.A.; Stark A.; Leptin M.; Furlong E.E.M.
A conserved role for Snail as a potentiator of active transcription
Genes & Development 28 (2): 167-181 (2014-01-15)


Bonn S.; Zinzen R.P.; Perez-Gonzalez A.; Riddell A.; Gavin A.C.; Furlong E.E.
Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP
Nature Protocols 7 (5): 978-994 (2012-05)

Bonn S.; Zinzen R.P.; Girardot C.; Gustafson E.H.; Perez-Gonzalez A.; Delhomme N.; Ghavi-Helm Y.; Wilczynski B.; Riddell A.; Furlong E.E.
Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
Nature Genetics 44 (2): 148-156 (2012-02)


Zinzen R.P.; Girardot C.; Gagneur J.; Braun M.; Furlong E.E.
Combinatorial binding predicts spatio-temporal cis-regulatory activity
Nature 462 (7269): 65-70 (2009-11-05)


Zinzen R.P.; Furlong E.E.
Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis
Genome Biology 9 (11): 240 (2008-11-04)


Goltsev Y.; Fuse N.; Frasch M.; Zinzen R.P.; Lanzaro G.; Levine M.
Evolution of the dorsal-ventral patterning network in the mosquito, Anopheles gambiae
Development 134 (13): 2415-2424 (2007-07)

Zinzen R.P.; Papatsenko D.
Enhancer responses to similarly distributed antagonistic gradients in development
PLoS Computational Biology 3 (5): e84 (2007-05-11)

Zeitlinger J.; Zinzen R.P.; Stark A.; Kellis M.; Zhang H.; Young R.A.; Levine M.
Whole-genome ChIP-chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo
Genes & Development 21 (4): 385-390 (2007-02-15)


Zinzen R.P.; Cande J.; Ronshaugen M.; Papatsenko D.; Levine M.
Evolution of the ventral midline in insect embryos
Developmental Cell 11 (6): 895-902 (2006-12)

Zinzen R.P.; Senger K.; Levine M.; Papatsenko D.
Computational models for neurogenic gene expression in the Drosophila embryo
Current Biology 16 (13): 1358-1365 (2006-07-11)

De Renzis S.; Yu J.; Zinzen R.P.; Wieschaus E.
Dorsal-ventral pattern of Delta trafficking is established by a Snail-Tom-Neuralized pathway
Developmental Cell 10 (2): 257-264 (2006-02)


Biemar F.; Zinzen R.P.; Ronshaugen M.; Sementchenko V.; Manak J.R.; Levine M.S.
Spatial regulation of microRNA gene expression in the Drosophila embryo
Proceedings of the National Academy of Sciences of the United States of America 102 (44): 15907-15911 (2005-11-01)


Markstein M.; Zinzen R.P.; Markstein P.; Yee K.P.; Erives A.; Stathopoulos A.; Levine M.
A regulatory code for neurogenic gene expression in the Drosophila embryo
Development 131 (10): 2387-2394 (2004-05)

Underwood D.H.; Zinzen R.P.; McEachern M.J.
Template requirements for telomerase translocation in Kluyveromyces lactis
Molecular and Cellular Biology 24 (2): 912-923 (2004-01)