Browse by Research Team

BMC Biology

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

Oxidative metabolism drives immortalization of neural stem cells during tumorigenesis.
Bonnay, F. and Veloso, A. and Steinmann, V. and Köcher, T. and Abdusselamoglu, M.D. and Bajaj, S. and Rivelles, E. and Landskron, L. and Esterbauer, H. and Zinzen, R.P. and Knoblich, J.A.
Cell 182 (6): 1490-1507. 17 September 2020

Current Biology

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

Current Opinion in Systems Biology

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

Development

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.
McCorkindale, A.L. and Wahle, P. and Werner, S. and Jungreis, I. and Menzel, P. and Shukla, C.J. and Abreu, R.L.P. and Irizarry, R.A. and Meyer, I.M. and Kellis, M. and Zinzen, R.P.
Development 146 (6): dev175265. 28 March 2019

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

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

Developmental Cell

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

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

EMBO Journal

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 (6): e98452. 15 March 2018

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

Genes & Development

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

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

Genome Biology

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

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

Journal of Biological Chemistry

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

Molecular Systems Biology

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

Molecular and Cellular Biology

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

Nature

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

Nature Communications

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

Nature Genetics

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

Nature Methods

Spatiotemporal, optogenetic control of gene expression in organoids.
Legnini, I. and Emmenegger, L. and Zappulo, A. and Rybak-Wolf, A. and Wurmus, R. and Oliveras Martinez, A. and Cerda Jara, C. and Boltengagen, A. and Hessler, T. and Mastrobuoni, G. and Kempa, S. and Zinzen, R. and Woehler, A. and Rajewsky, N.
Nature Methods 20 (10): 1544-1552. October 2023

Nature Protocols

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

Nucleic Acids Research

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
Glaser, L.V. and Steiger, M. and Fuchs, A. and van Bömmel, A. and Einfeldt, E. and Chung, H.R. and Vingron, M. and Meijsing, S.H.
Nucleic Acids Research 49 (21): 12178-12195. 2 December 2021

PLoS Computational Biology

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

Proceedings of the National Academy of Sciences of the United States of America

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

RNA Biology

Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis.
Menzel, P. and McCorkindale, A.L. and Stefanov, S.R. and Zinzen, R.P. and Meyer, I.M.
RNA Biology 16 (1): 69-81. 20 January 2019

Science

Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly.
Li, H. and Janssens, J. and De Waegeneer, M. and Kolluru, S.S. and Davie, K. and Gardeux, V. and Saelens, W. and David, F.P.A. and Brbić, M. and Spanier, K. and Leskovec, J. and McLaughlin, C.N. and Xie, Q. and Jones, R.C. and Brueckner, K. and Shim, J. and Tattikota, S.G. and Schnorrer, F. and Rust, K. and Nystul, T.G. and Carvalho-Santos, Zi. and Ribeiro, C. and Pal, S. and Mahadevaraju, S. and Przytycka, T.M. and Allen, A.M. and Goodwin, S.F. and Berry, C.W. and Fuller, M.T. and White-Cooper, H. and Matunis, E.L. and DiNardo, S. and Galenza, A. and O'Brien, L.E. and Dow, J.A.T. and Jasper, H. and Oliver, B. and Perrimon, N. and Deplancke, B. and Quake, S.R. and Luo, L. and Aerts, S.
Science 375 (6584): eabk2432. 4 March 2022

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

Science of the Total Environment

SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution.
Schumann, V.F. and de Castro Cuadrat, R.R. and Wyler, E. and Wurmus, R. and Deter, A. and Quedenau, C. and Dohmen, J. and Faxel, M. and Borodina, T. and Blume, A. and Freimuth, J. and Meixner, M. and Grau, J.H. and Liere, K. and Hackenbeck, T. and Zietzschmann, F. and Gnirss, R. and Böckelmann, U. and Uyar, B. and Franke, V. and Barke, N. and Altmüller, J. and Rajewsky, N. and Landthaler, M. and Akalin, A.
Science of the Total Environment 853 : 158931. 20 December 2022

Scientific Reports

Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz.
Race, A.M. and Fuchs, A. and Chung, H.R.
Scientific Reports 13 (1): 22020. 12 December 2023

bioRxiv

Spatio-temporal, optogenetic control of gene expression in organoids.
Legnini, I. and Emmenegger, L. and Zappulo, A. and Wurmus, R. and Oliveras Martinez, A. and Cerda Jara, C. and Boltengagen, A. and Hessler, T. and Mastrobuoni, G. and Rybak-Wolf, A. and Kempa, S. and Zinzen, R.P. and Woehler, A. and Rajewsky, N.
bioRxiv : 2021.09.26.461850v3. 9 February 2022

Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
Glaser, L.V. and Steiger, M. and Fuchs, A. and van Bömmel, A. and Einfeldt, E. and Chung, H.R. and Vingron, M. and Meijsing, S.H.
bioRxiv : 2021.06.04.446899. 6 June 2021

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.
McCorkindale, A.L. and Wahle, P. and Werner, S. and Jungreis, I. and Menzel, P. and Shukla, C.J. and Lopes Pereira Abreu, R. and Irizarry, Rafael and Meyer, I. and Kellis, Manolis and Zinzen, R.P.
bioRxiv : 483461. 27 December 2018

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

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

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