Vedran Franke

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Altuna AkalinMax Delbrück Center for Molecular MedicineVerified email at mdc-berlin.de
Kristian VlahovicekUniversity of Zagreb - Faculty of Science - Department of Biology - Bioinformatics GroupVerified email at biol.pmf.hr
Petr SvobodaInstitute of Molecular Genetics of the Czech Academy of SciencesVerified email at img.cas.cz
Nikolaus RajewskyProfessor, Systems Biology, Max Delbruck Center for Molecular Medicine, BerlinVerified email at mdc-berlin.de
Emanuel WylerPostdoc, Berlin Institute for Medical Systems Biology, Max Delbruck Center for MolecularVerified email at mdc-berlin.de
Markus LandthalerMax-Delbrück-Center for Molecular Medicine Berlin, Biologie Humboldt-Universität zu BerlinVerified email at mdc-berlin.de
Bora UyarMax Delbrueck Center for Molecular Medicine - The Berlin Institute for Medical Systems BiologyVerified email at mdc-berlin.de
Matthias SelbachProfessor, Max Delbruck Center for Molecular MedicineVerified email at mdc-berlin.de
Jonathan RonenMax Delbruck Center for Molecular Medicine, BerlinVerified email at mdc-berlin.de
Boris LenhardImperial College LondonVerified email at imperial.ac.uk
WFJ van IJckenAssistant Professor, Erasmus MCVerified email at erasmusmc.nl
Marina ChekulaevaMax Delbrück Center for Molecular MedicineVerified email at mdc-berlin.de
Koshi ImamiRIKEN Center for Integrative Medical Sciences (IMS)Verified email at riken.jp
Camilla Ciolli MattioliWeizmann Institute of ScienceVerified email at weizmann.ac.il
Erik McShanePostdoctoral Fellow at Harvard Medical SchoolVerified email at hms.harvard.edu
Rosa KarlicPostdoc, University of Zagreb, Faculty of Science, Department of Biology, Division of MolecularVerified email at biol.pmf.hr
Roberto ArsièMax Delbrück Center for Molecular Medicine, BerlinVerified email at mdc-berlin.de
Jan Christian BryneGoogleVerified email at bryne.name
Frank GrosveldProfessor Cell Biology ErasmusMCVerified email at erasmusmc.nl
Jan DohmenHamburg University of TechnologyVerified email at tuhh.de

Vedran Franke

Max Delbrueck Center

Verified email at mdc-berlin.de

Functional Genomics


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A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes M Flemr, R Malik, V Franke, J Nejepinska, R Sedlacek, K Vlahovicek, ... Cell 155 (4), 807-816, 2013	325	2013
Genomation: a toolkit to summarize, annotate and visualize genomic intervals A Akalin, V Franke, K Vlahoviček, CE Mason, D Schübeler Bioinformatics 31 (7), 1127-1129, 2015	291	2015
Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy E Wyler, K Mösbauer, V Franke, A Diag, LT Gottula, R Arsiè, F Klironomos, ... IScience 24 (3), 2021	274*	2021
RNA localization is a key determinant of neurite-enriched proteome A Zappulo, D Van Den Bruck, C Ciolli Mattioli, V Franke, K Imami, ... Nature communications 8 (1), 583, 2017	214	2017
Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells M Kim, V Franke, B Brandt, ED Lowenstein, V Schöwel, S Spuler, A Akalin, ... Nature communications 11 (1), 6375, 2020	181	2020
The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3′ processing K Abe, R Yamamoto, V Franke, M Cao, Y Suzuki, MG Suzuki, ... The EMBO journal 34 (11), 1523-1537, 2015	162	2015
Cell-type specialization is encoded by specific chromatin topologies W Winick-Ng, A Kukalev, I Harabula, L Zea-Redondo, D Szabó, M Meijer, ... Nature 599 (7886), 684-691, 2021	161	2021
A cohesin-independent role for NIPBL at promoters provides insights in CdLS J Zuin, V Franke, WFJ van IJcken, A Van Der Sloot, ID Krantz, ... PLoS genetics 10 (2), e1004153, 2014	153	2014
Sculpting the transcriptome during the oocyte-to-embryo transition in mouse P Svoboda, V Franke, RM Schultz Current topics in developmental biology 113, 305-349, 2015	143	2015
Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes V Franke, S Ganesh, R Karlic, R Malik, J Pasulka, F Horvat, M Kuzman, ... Genome research 27 (8), 1384-1394, 2017	140	2017
Alternative 3′ UTRs direct localization of functionally diverse protein isoforms in neuronal compartments C Ciolli Mattioli, A Rom, V Franke, K Imami, G Arrey, M Terne, A Woehler, ... Nucleic acids research 47 (5), 2560-2573, 2019	125	2019
Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program E Wyler, V Franke, J Menegatti, C Kocks, A Boltengagen, S Praktiknjo, ... Nature communications 10 (1), 4878, 2019	120	2019
The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner F Sleutels, W Soochit, M Bartkuhn, H Heath, S Dienstbach, P Bergmaier, ... Epigenetics & chromatin 5, 1-21, 2012	102	2012
PiGx: reproducible genomics analysis pipelines with GNU Guix R Wurmus, B Uyar, B Osberg, V Franke, A Gosdschan, K Wreczycka, ... Gigascience 7 (12), giy123, 2018	67	2018
HOT or not: examining the basis of high-occupancy target regions K Wreczycka, V Franke, B Uyar, R Wurmus, S Bulut, B Tursun, A Akalin Nucleic acids research 47 (11), 5735-5745, 2019	64	2019
Long non-coding RNA exchange during the oocyte-to-embryo transition in mice R Karlic, S Ganesh, V Franke, E Svobodova, J Urbanova, Y Suzuki, F Aoki, ... Dna research 24 (2), 129-141, 2017	59	2017
Identifying tumor cells at the single-cell level using machine learning J Dohmen, A Baranovskii, J Ronen, B Uyar, V Franke, A Akalin Genome Biology 23 (1), 123, 2022	48	2022
Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection E Wyler, J Menegatti, V Franke, C Kocks, A Boltengagen, T Hennig, ... Genome Biology 18, 1-19, 2017	46	2017
PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC LM Appel, V Franke, M Bruno, I Grishkovskaya, A Kasiliauskaite, ... Nature Communications 12 (1), 6078, 2021	43	2021
A novel complex, RUNX1-MYEF2, represses hematopoietic genes in erythroid cells B van Riel, T Pakozdi, R Brouwer, R Monteiro, K Tuladhar, V Franke, ... Molecular and cellular biology 32 (19), 3814-3822, 2012	42	2012

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