Article
Amyloid precursor protein ortholog Appl acts with Vnd during mushroom body axon growth in Drosophila.
Marquilly, Claire, Busto, Germain U., Pasquer, Laure, Zinzen, Robert P. 
ORCID: https://orcid.org/0000-0002-8638-5102, Hassan, Bassem A., Fradkin, Lee G., Preat, Thomas, Boulanger, Ana and Dura, Jean-Maurice ORCID: https://orcid.org/0000-0001-8296-9023
Genetics 233
(3): iyag112.
July 2026
RoCK and ROI: single-cell transcriptomics with multiplexed enrichment of selected transcripts and region-specific sequencing.
Moro, Giulia ORCID: https://orcid.org/0000-0002-0642-6294, Mallona, Izaskun ORCID: https://orcid.org/0000-0002-2853-7526, Barz, Malwine J., Maillard, Joël, Brügger, Michael David, Fazilaty, Hassan ORCID: https://orcid.org/0000-0002-9387-0413, Szabo, Quentin ORCID: https://orcid.org/0000-0002-3539-7875, Valenta, Tomas ORCID: https://orcid.org/0000-0002-3043-1835, Handler, Kristina, Kerlin, Fiona ORCID: https://orcid.org/0009-0008-3517-0911, Bastian, Lorenz ORCID: https://orcid.org/0000-0002-1487-9437, Baldus, Claudia D. ORCID: https://orcid.org/0000-0002-0748-834X, Moor, Andreas E. ORCID: https://orcid.org/0000-0001-8715-8449, Zinzen, Robert ORCID: https://orcid.org/0000-0002-8638-5102, Robinson, Mark D. ORCID: https://orcid.org/0000-0002-3048-5518, Brunner, Erich ORCID: https://orcid.org/0000-0002-9712-9040 and Basler, Konrad
Nature Communications 16
(1): 10991.
10 December 2025
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. ORCID: https://orcid.org/0009-0007-4891-1734, Haunold, T., Cepraga, A., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, Krüger, M., Petsalaki, E., Wang, Y.C. and Leptin, M.
eLife 13
: e99263.
3 October 2024
Visualization and data exploration of chromosome conformation capture data using Voronoi diagrams with v3c-viz.
Race, A.M., Fuchs, A. ORCID: https://orcid.org/0000-0002-0464-9064 and Chung, H.R.
Scientific Reports 13
(1): 22020.
12 December 2023
Spatiotemporal, optogenetic control of gene expression in organoids.
Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Emmenegger, L. ORCID: https://orcid.org/0000-0003-2165-7944, Zappulo, A., Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Oliveras Martinez, A. ORCID: https://orcid.org/0000-0002-5880-5245, Cerda Jara, C. ORCID: https://orcid.org/0000-0003-1783-5533, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Hessler, T., Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Zinzen, R. ORCID: https://orcid.org/0000-0002-8638-5102, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature Methods 20
(10): 1544-1552.
October 2023
Fly Cell Atlas: a single-nucleus transcriptomic atlas of the adult fruit fly.
Li, H. ORCID: https://orcid.org/0000-0002-7332-7122, Janssens, J. ORCID: https://orcid.org/0000-0001-9264-0782, De Waegeneer, M. ORCID: https://orcid.org/0000-0002-4535-3737, Kolluru, S.S., Davie, K. ORCID: https://orcid.org/0000-0003-2182-1249, Gardeux, V. ORCID: https://orcid.org/0000-0001-8954-2161, Saelens, W. ORCID: https://orcid.org/0000-0002-7114-6248, David, F.P.A. ORCID: https://orcid.org/0000-0001-8539-865X, Brbić, M. ORCID: https://orcid.org/0000-0002-1120-1778, Spanier, K. ORCID: https://orcid.org/0000-0002-1375-4157, Leskovec, J. ORCID: https://orcid.org/0000-0002-5411-923X, McLaughlin, C.N. ORCID: https://orcid.org/0000-0002-7518-8920, Xie, Q. ORCID: https://orcid.org/0000-0002-0997-8326, Jones, R.C. ORCID: https://orcid.org/0000-0001-7235-9854, Brueckner, K., Shim, J. ORCID: https://orcid.org/0000-0003-2409-1130, Tattikota, S.G. ORCID: https://orcid.org/0000-0003-0318-5533, Schnorrer, F. ORCID: https://orcid.org/0000-0002-9518-7263, Rust, K. ORCID: https://orcid.org/0000-0001-6367-5994, Nystul, T.G. ORCID: https://orcid.org/0000-0002-6250-2394, Carvalho-Santos, Zi. ORCID: https://orcid.org/0000-0001-7100-308X, Ribeiro, C. ORCID: https://orcid.org/0000-0002-9542-7335, Pal, S. ORCID: https://orcid.org/0000-0003-4840-3944, Mahadevaraju, S. ORCID: https://orcid.org/0000-0002-2807-5237, Przytycka, T.M. ORCID: https://orcid.org/0000-0002-6261-277X, Allen, A.M. ORCID: https://orcid.org/0000-0002-7961-4392, Goodwin, S.F. ORCID: https://orcid.org/0000-0002-0552-4140, Berry, C.W. ORCID: https://orcid.org/0000-0003-1096-2804, Fuller, M.T. ORCID: https://orcid.org/0000-0002-3804-4987, White-Cooper, H. ORCID: https://orcid.org/0000-0002-3373-8023, Matunis, E.L. ORCID: https://orcid.org/0000-0001-5439-4656, DiNardo, S. ORCID: https://orcid.org/0000-0003-4131-5511, Galenza, A. ORCID: https://orcid.org/0000-0001-9038-9483, O'Brien, L.E., Dow, J.A.T. ORCID: https://orcid.org/0000-0002-9595-5146, Jasper, H., Oliver, B. ORCID: https://orcid.org/0000-0002-3455-4891, Perrimon, N. ORCID: https://orcid.org/0000-0001-7542-472X, Deplancke, B. ORCID: https://orcid.org/0000-0001-9935-843X, Quake, S.R. ORCID: https://orcid.org/0000-0002-1613-0809, Luo, L. ORCID: https://orcid.org/0000-0001-5467-9264 and Aerts, S. ORCID: https://orcid.org/0000-0002-8006-0315
Science 375
(6584): eabk2432.
4 March 2022
Assessing genome-wide dynamic changes in enhancer activity during early mESC differentiation by FAIRE-STARR-seq.
Glaser, L.V. ORCID: https://orcid.org/0000-0002-4495-9032, Steiger, M. ORCID: https://orcid.org/0000-0002-3747-685X, Fuchs, A. ORCID: https://orcid.org/0000-0002-0464-9064, van Bömmel, A., Einfeldt, E., Chung, H.R. ORCID: https://orcid.org/0000-0002-4132-0911, Vingron, M. and Meijsing, S.H. ORCID: https://orcid.org/0000-0002-8095-1847
Nucleic Acids Research 49
(21): 12178-12195.
2 December 2021
Oxidative metabolism drives immortalization of neural stem cells during tumorigenesis.
Bonnay, F., Veloso, A. ORCID: https://orcid.org/0000-0002-2369-4688, Steinmann, V., Köcher, T., Abdusselamoglu, M.D. ORCID: https://orcid.org/0000-0001-8467-3947, Bajaj, S., Rivelles, E., Landskron, L. ORCID: https://orcid.org/0000-0003-0405-2046, Esterbauer, H., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 and Knoblich, J.A.
Cell 182
(6): 1490-1507.
17 September 2020
A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.
McCorkindale, A.L. ORCID: https://orcid.org/0000-0002-0840-0784, Wahle, P. ORCID: https://orcid.org/0000-0002-4728-806X, Werner, S. ORCID: https://orcid.org/0000-0001-8350-2417, Jungreis, I., Menzel, P. ORCID: https://orcid.org/0000-0003-4964-0685, Shukla, C.J., Abreu, R.L.P., Irizarry, R.A., Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479, Kellis, M. and Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102
Development 146
(6): dev175265.
28 March 2019
Transcriptional dynamics of microRNAs and their targets during Drosophila neurogenesis.
Menzel, P. ORCID: https://orcid.org/0000-0003-4964-0685, McCorkindale, A.L. ORCID: https://orcid.org/0000-0002-0840-0784, Stefanov, S.R. ORCID: https://orcid.org/0000-0003-4341-8725, Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 and Meyer, I.M. ORCID: https://orcid.org/0000-0002-4048-3479
RNA Biology 16
(1): 69-81.
20 January 2019
Determinants of promoter and enhancer transcription directionality in metazoans.
Ibrahim, M.M. ORCID: https://orcid.org/0000-0001-6954-5314, Karabacak, A. ORCID: https://orcid.org/0000-0002-4740-7938, Glahs, A. ORCID: https://orcid.org/0000-0003-0721-3757, Kolundzic, E. ORCID: https://orcid.org/0000-0002-7811-3174, Hirsekorn, A., Carda, A., Tursun, B. ORCID: https://orcid.org/0000-0001-7293-8629, Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, Lacadie, S.A. ORCID: https://orcid.org/0000-0002-0893-5340 and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Nature Communications 9
(1): 4472.
26 October 2018
High-throughput identification of RNA nuclear enrichment sequences.
Shukla, C.J., McCorkindale, A.L. ORCID: https://orcid.org/0000-0002-0840-0784, Gerhardinger, C., Korthauer, K.D. ORCID: https://orcid.org/0000-0002-4565-1654, Cabili, M.N., Shechner, D.M., Irizarry, R.A., Maass, P. ORCID: https://orcid.org/0000-0002-2742-8301 and Rinn, J.L. ORCID: https://orcid.org/0000-0002-7231-7539
EMBO Journal 37
(6): e98452.
15 March 2018
McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.
Hafez, D., Karabacak, A. ORCID: https://orcid.org/0000-0002-4740-7938, Krueger, S., Hwang, Y.C., Wang, L.S., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 and Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116
Genome Biology 18
(1): 199.
26 October 2017
The Drosophila embryo at single-cell transcriptome resolution.
Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Wahle, P. ORCID: https://orcid.org/0000-0002-4728-806X, Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Kipar, C., Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102
Science 358
(6360): 194-199.
13 October 2017
Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Praktiknjo, S.D. ORCID: https://orcid.org/0000-0002-0186-5271, Grosswendt, S. ORCID: https://orcid.org/0000-0001-7722-2937, Wahle, P. ORCID: https://orcid.org/0000-0002-4728-806X, Ruffault, P.L. ORCID: https://orcid.org/0000-0002-3378-3828, Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Schreyer, L., Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872, Zinzen, R. ORCID: https://orcid.org/0000-0002-8638-5102, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
BMC Biology 15
(1): 44.
19 May 2017
Differential dynamics of the mammalian mRNA and protein expression response to misfolding stress.
Cheng, Z. ORCID: https://orcid.org/0000-0002-1353-2976, 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
miR-184 regulates pancreatic β-cell function according to glucose metabolism.
Tattikota, S.G. ORCID: https://orcid.org/0000-0003-0318-5533, Rathjen, T., Hausser, J., Khedkar, A., Kabra, U.D., Pandey, V.K., Sury, M.D., Wessels, H.H. ORCID: https://orcid.org/0000-0001-5551-404X, Mollet, I.G., Eliasson, L., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, Zavolan, M., Kadener, S., Tschöp, M., Jastroch, M., Friedländer, M.R. ORCID: https://orcid.org/0000-0001-6577-4363 and Poy, M.N. ORCID: https://orcid.org/0000-0002-4904-2426
Journal of Biological Chemistry 290
(33): 20284-20294.
14 August 2015
A conserved role for Snail as a potentiator of active transcription.
Rembold, M., Ciglar, L., Yáñez-Cuna, J.O., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, 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
Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP.
Bonn, S., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, 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. ORCID: https://orcid.org/0000-0002-8638-5102, 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
Combinatorial binding predicts spatio-temporal cis-regulatory activity.
Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, Girardot, C., Gagneur, J., Braun, M. and Furlong, E.E.
Nature 462
(7269): 65-70.
5 November 2009
Evolution of the dorsal-ventral patterning network in the mosquito, Anopheles gambiae.
Goltsev, Y., Fuse, N., Frasch, M., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, Lanzaro, G. and Levine, M.
Development 134
(13): 2415-2424.
July 2007
Enhancer responses to similarly distributed antagonistic gradients in development.
Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 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. ORCID: https://orcid.org/0000-0002-8638-5102, Stark, A., Kellis, M., Zhang, H., Young, R.A. and Levine, M.
Genes & Development 21
(4): 385-390.
15 February 2007
Evolution of the ventral midline in insect embryos.
Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, 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. ORCID: https://orcid.org/0000-0002-8638-5102, 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. ORCID: https://orcid.org/0000-0002-8638-5102 and Wieschaus, E.
Developmental Cell 10
(2): 257-264.
February 2006
Spatial regulation of microRNA gene expression in the Drosophila embryo.
Biemar, F., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, 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
A regulatory code for neurogenic gene expression in the Drosophila embryo.
Markstein, M., Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, 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. ORCID: https://orcid.org/0000-0002-8638-5102 and McEachern, M.J.
Molecular and Cellular Biology 24
(2): 912-923.
January 2004
Review
Divergence in cis-regulatory networks: taking the 'species' out of cross-species analysis.
Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102 and Furlong, E.E.
Genome Biology 9
(11): 240.
4 November 2008
Editorial
Editorial overview.
Shvartsman, S. and Zinzen, R. ORCID: https://orcid.org/0000-0002-8638-5102
Current Opinion in Systems Biology 11
: v.
October 2018
Putting chromatin in its place: the pioneer factor NeuroD1 modulates chromatin state to drive cell fate decisions.
Glahs, A. ORCID: https://orcid.org/0000-0003-0721-3757 and Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102
EMBO Journal 35
(1): 1-3.
4 January 2016
Preprint
Evolutionarily conserved transcriptional regulators control monoaminergic neuron development.
Lewis, Clifton ORCID: https://orcid.org/0000-0002-3077-8150, Goulty, Matthew ORCID: https://orcid.org/0009-0001-5731-6722, Wroblewska, Aniela, Croxall, Nicola ORCID: https://orcid.org/0009-0003-1061-6909, Onion, David ORCID: https://orcid.org/0000-0002-4522-2307, Robinson, Sue, Zinzen, Robert P. ORCID: https://orcid.org/0000-0002-8638-5102, Solana, Jordi ORCID: https://orcid.org/0000-0002-6770-3929, Kyriacou, Charalambos P. ORCID: https://orcid.org/0000-0003-4889-7606, Rosato, Ezio ORCID: https://orcid.org/0000-0001-7297-4697 and Feuda, Roberto ORCID: https://orcid.org/0000-0003-0857-1732
bioRxiv
: 2025.10.29.685200v2.
31 October 2025
Non-autonomous Vnd acts with autonomous Appl during mushroom body axon growth in Drosophila.
Marquilly, Claire, Boulanger, Ana, Busto, Germain U., Zinzen, Robert P. ORCID: https://orcid.org/0000-0002-8638-5102, Hassan, Bassem A., Fradkin, Lee G. and Dura, Jean-Maurice
bioRxiv
: 2023.09.01.555727v2.
31 July 2025
Dissecting the role of RNA-binding proteins in early herpes simplex virus 1 transcription using acute protein depletion.
Barke, N ORCID: https://orcid.org/0009-0004-5862-6628, Masser, S., Stalling, D., Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102, Schreiner, S., Bosse, J. and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
bioRxiv
: 2025.02.10.637450.
11 February 2025
High-resolution molecular atlas of a lung tumor in 3D.
Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Schallenberg, Simon, León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Theurillat, I. ORCID: https://orcid.org/0000-0002-1125-1951, Thomas, G., Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Fritzsche, S. ORCID: https://orcid.org/0000-0003-3335-3534, Nimo, J. ORCID: https://orcid.org/0000-0002-1565-7799, Ruff, L., Dernbach, G., Jurmeister, P., Murphy, S., Gregory, M., Liang, Y., Cordenonsi, M., Piccolo, S., Coscia, F. ORCID: https://orcid.org/0000-0002-2244-5081, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Klauschen, F. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
bioRxiv
: 2023.05.10.539644.
10 May 2023
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