Browse by Research Team

2025

Dissecting the role of RNA-binding proteins in early herpes simplex virus 1 transcription using acute protein depletion.
Barke, N, Masser, S., Stalling, D., Wyler, E., Zinzen, R.P., Schreiner, S., Bosse, J. and Landthaler, M.
bioRxiv : 2025.02.10.637450. 11 February 2025

2024

Differential regulation of the proteome and phosphoproteome along the dorso-ventral axis of the early Drosophila embryo.
Gomez, J.M., Nolte, H., Vogelsang, E., Dey, B., Takeda, M., Giudice, G., Faxel, M., Haunold, T., Cepraga, A., Zinzen, R.P., Krüger, M., Petsalaki, E., Wang, Y.C. and Leptin, M.
eLife 13 : e99263. 3 October 2024

RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.
Moro, G., Mallona, I., Maillard, J., Brügger, M.D., Fazilaty, H., Szabo, Q., Valenta, T., Handler, K., Kerlin, F., Moor, A.E., Zinzen, R., Robinson, M.D., Brunner, E. and Basler, K.
bioRxiv : 2024.05.18.594120v2. 3 June 2024

2023

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

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

High-resolution molecular atlas of a lung tumor in 3D.
Pentimalli, T.M., Schallenberg, Simon, León-Periñán, D., Legnini, I., Theurillat, I., Thomas, G., Boltengagen, A., Fritzsche, S., Nimo, J., Ruff, L., Dernbach, G., Jurmeister, P., Murphy, S., Gregory, M., Liang, Y., Cordenonsi, M., Piccolo, S., Coscia, F., Woehler, A., Karaiskos, N., Klauschen, F. and Rajewsky, N.
bioRxiv : 2023.05.10.539644. 10 May 2023

2022

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

2021

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

2020

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

2019

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

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

2018

Determinants of promoter and enhancer transcription directionality in metazoans.
Ibrahim, M.M., Karabacak, A., Glahs, A., Kolundzic, E., Hirsekorn, A., Carda, A., Tursun, B., Zinzen, R.P., 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., McCorkindale, A.L., Gerhardinger, C., Korthauer, K.D., Cabili, M.N., Shechner, D.M., Irizarry, R.A., Maass, P. and Rinn, J.L.
EMBO Journal 37 (6): e98452. 15 March 2018

2017

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

The Drosophila embryo at single-cell transcriptome resolution.
Karaiskos, N., Wahle, P., Alles, J., Boltengagen, A., Ayoub, S., Kipar, C., Kocks, C., 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., Karaiskos, N., Praktiknjo, S.D., Grosswendt, S., Wahle, P., Ruffault, P.L., Ayoub, S., Schreyer, L., Boltengagen, A., Birchmeier, C., Zinzen, R., Kocks, C. and Rajewsky, N.
BMC Biology 15 (1): 44. 19 May 2017

2016

Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.
Cheng, Z., Teo, G., Krueger, S., Rock, T.M., Koh, H.W.L., 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

miR-184 regulates pancreatic β-cell function according to glucose metabolism.
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., Tschöp, M., Jastroch, M., 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., Ciglar, L., Yáñez-Cuna, J.O., Zinzen, R.P., Girardot, C., Jain, A., Welte, M.A., Stark, A., 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., Zinzen, R.P., Perez-Gonzalez, A., Riddell, A., 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., Zinzen, R.P., Girardot, C., Gustafson, E.H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczynski, B., 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., Girardot, C., Gagneur, J., 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., Fuse, N., Frasch, M., Zinzen, R.P., 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., Zinzen, R.P., Stark, A., Kellis, M., Zhang, H., 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., Cande, J., Ronshaugen, M., 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., Senger, K., 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., Yu, J., 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., Zinzen, R.P., Ronshaugen, M., Sementchenko, V., 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., Zinzen, R.P., Markstein, P., Yee, K.P., Erives, A., Stathopoulos, A. and Levine, M.
Development 131 (10): 2387-2394. May 2004

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