Personal information

genomics, bioinformatics, seqeuncing, data analysis, statistics
Germany

Activities

Employment (1)

Max Delbrück Centrum für Molekulare Medizin Berlin Buch: Berlin-Buch, Berlin, DE

2014-11-01 to present | post doc (BIMSB)
Employment
Source: Self-asserted source
Vedran Franke

Education and qualifications (1)

Zagreb University Faculty of Science: Zagreb, HR

2010-05 to 2014-11 | PhD (Department for Molecular Biology)
Education
Source: Self-asserted source
Vedran Franke

Works (34)

Herpesviruses mimic zygotic genome activation to promote viral replication

Nature Communications
2025-01-16 | Journal article
Contributors: Eva Neugebauer; Stephanie Walter; Jiang Tan; Nir Drayman; Vedran Franke; Michiel van Gent; Sandra Pennisi; Pia Veratti; Karla S. Stein; Isabelle Welker et al.
Source: check_circle
Crossref

Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond

2024-07-18 | Preprint
Contributors: Bora Uyar; Taras Savchyn; Ricardo Wurmus; Ahmet Sarigun; Mohammed Maqsood Shaik; Vedran Franke; Altuna Akalin
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Crossref

A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons

2024-05-12 | Preprint
Contributors: Dominik Szabó; Vedran Franke; Simona Bianco; Mykhailo Y. Batiuk; Eleanor J. Paul; Alexander Kukalev; Ulrich G. Pfisterer; Ibai Irastorza-Azcarate; Andrea M. Chiariello; Samuel Demharter et al.
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Crossref

The SPOC proteins DIDO3 and PHF3 co-regulate gene expression and neuronal differentiation

Nature Communications
2023-11-30 | Journal article
Contributors: Johannes Benedum; Vedran Franke; Lisa-Marie Appel; Lena Walch; Melania Bruno; Rebecca Schneeweiss; Juliane Gruber; Helena Oberndorfer; Emma Frank; Xué Strobl et al.
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Crossref

Transcriptional reprogramming by mutated IRF4 in lymphoma

Nature Communications
2023-11-07 | Journal article
Contributors: Nikolai Schleussner; Pierre Cauchy; Vedran Franke; Maciej Giefing; Oriol Fornes; Naveen Vankadari; Salam A. Assi; Mariantonia Costanza; Marc A. Weniger; Altuna Akalin et al.
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Crossref

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators

Nature Communications
2023-01-11 | Journal article
Contributors: Lisa-Marie Appel; Vedran Franke; Johannes Benedum; Irina Grishkovskaya; Xué Strobl; Anton Polyansky; Gregor Ammann; Sebastian Platzer; Andrea Neudolt; Anna Wunder et al.
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Crossref

A new type of transcriptional reprogramming by an IRF4 mutation in lymphoma

2022-12-29 | Preprint
Contributors: Nikolai Schleussner; Pierre Cauchy; Vedran Franke; Maciej Giefing; Oriol Fornes; Naveen Vankadari; Salam Assi; Mariantonia Costanza; Marc A. Weniger; Altuna Akalin et al.
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Crossref

Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction

Cancers
2022-11-15 | Journal article
Contributors: Artem Baranovskii; Irem B. Gündüz; Vedran Franke; Bora Uyar; Altuna Akalin
Source: check_circle
Crossref
grade
Preferred source (of 2)‎

Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction

2022-06-17 | Preprint
Contributors: Artem Baranovskii; Irem B. Gunduz; Vedran Franke; Bora Uyar; Altuna Akalin
Source: check_circle
Crossref

The SPOC domain is a phosphoserine binding module that bridges transcription machinery with co- and post-transcriptional regulators

2022-02-27 | Preprint
Contributors: Lisa-Marie Appel; Irina Grishkovskaya; Johannes Benedum; Vedran Franke; Anton Polyansky; Andrea Neudolt; Anna Wunder; Bojan Zagrovic; Altuna Akalin; Kristina Djinovic-Carugo et al.
Source: check_circle
Crossref

PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC

Nature Communications
2021-10-19 | Journal article
Contributors: Lisa-Marie Appel; Vedran Franke; Melania Bruno; Irina Grishkovskaya; Aiste Kasiliauskaite; Tanja Kaufmann; Ursula E. Schoeberl; Martin G. Puchinger; Sebastian Kostrhon; Carmen Ebenwaldner et al.
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Crossref

Identifying tumor cells at the single cell level

2021-10-16 | Other
Contributors: Jan Dohmen; Artem Baranovskii; Jonathan Ronen; Bora Uyar; Vedran Franke; Altuna Akalin
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Crossref

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy

iScience
2021-03 | Journal article
Contributors: Emanuel Wyler; Kirstin Mösbauer; Vedran Franke; Asija Diag; Lina Theresa Gottula; Roberto Arsiè; Filippos Klironomos; David Koppstein; Katja Hönzke; Salah Ayoub et al.
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Crossref

Herpesviral induction of germline transcription factor DUX4 is critical for viral gene expression

2021-03-24 | Preprint
Contributors: Stephanie Walter; Vedran Franke; Nir Drayman; Emanuel Wyler; Savaş Tay; Markus Landthaler; Altuna Akalin; Armin Ensser; Florian Full
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Crossref

Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells

Nature Communications
2020-12-11 | Journal article
Contributors: Minchul Kim; Vedran Franke; Bettina Brandt; Elijah D. Lowenstein; Verena Schöwel; Simone Spuler; Altuna Akalin; Carmen Birchmeier
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Crossref

Bulk and single-cell gene expression profiling of SARS-CoV-2 infected human cell lines identifies molecular targets for therapeutic intervention

2020-05-05 | Preprint
Contributors: Wyler Emanuel; Mösbauer Kirstin; Franke Vedran; Diag Asija; Gottula Lina Theresa; Arsie Roberto; Klironomos Filippos; Koppstein David; Ayoub Salah; Buccitelli Christopher et al.
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Crossref

PHF3 regulates neuronal gene expression through the new Pol II CTD reader domain SPOC

2020-02-12 | Preprint
Contributors: Lisa-Marie Appel; Vedran Franke; Melania Bruno; Irina Grishkovskaya; Aiste Kasiliauskaite; Ursula E. Schoeberl; Martin G. Puchinger; Sebastian Kostrhon; Etienne Beltzung; Karl Mechtler et al.
Source: check_circle
Crossref

Autocrine LTA signaling drives NF-κB and JAK-STAT activity and myeloid gene expression in Hodgkin lymphoma

Blood
2019-03-28 | Journal article
Contributors: Linda von Hoff; Eva Kärgel; Vedran Franke; Erik McShane; Kathrin W. Schulz-Beiss; Giannino Patone; Nikolai Schleussner; Marina Kolesnichenko; Norbert Hübner; Oliver Daumke et al.
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Crossref

Single-cell RNA-sequencing of Herpes simplex virus 1-infected cells identifies NRF2 activation as an antiviral program

2019-03-04 | Other
Contributors: Emanuel Wyler; Vedran Franke; Jennifer Menegatti; Kocks Christine; Anastasiya Boltengagen; Samantha Praktiknjo; Barbara Walch-Rückheim; Nikolaus Rajewsky; Friedrich Grässer; Altuna Akalin et al.
Source: check_circle
Crossref

PiGx: reproducible genomics analysis pipelines with GNU Guix

GigaScience
2018-12-01 | Journal article
Contributors: Ricardo Wurmus; Bora Uyar; Brendan Osberg; Vedran Franke; Alexander Gosdschan; Katarzyna Wreczycka; Jonathan Ronen; Altuna Akalin
Source: check_circle
Crossref

Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes.

2017-05 | Journal article
Contributors: Franke V; Ganesh S; Karlic R; Malik R; Pasulka J; Horvat F; Kuzman M; Fulka H; Cernohorska M; Urbanova J et al.
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

Long non-coding RNA exchange during the oocyte-to-embryo transition in mice.

2017-04 | Journal article
Contributors: Karlic R; Ganesh S; Franke V; Svobodova E; Urbanova J; Suzuki Y; Aoki F; Vlahovicek K; Svoboda P
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

Sculpting the Transcriptome During the Oocyte-to-Embryo Transition in Mouse.

2015 | Journal article
Contributors: Svoboda P; Franke V; Schultz RM
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

Maternal SIN3A regulates reprogramming of gene expression during mouse preimplantation development.

2015-10 | Journal article
Contributors: Jimenez R; Melo EO; Davydenko O; Ma J; Mainigi M; Franke V; Schultz RM
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

The first murine zygotic transcription is promiscuous and uncoupled from splicing and 3' processing.

2015-06 | Journal article
DOI:

10.15252/embj.201490648

PMID:

25896510

Contributors: Abe K; Yamamoto R; Franke V; Cao M; Suzuki Y; Suzuki MG; Vlahovicek K; Svoboda P; Schultz RM; Aoki F
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

Genomation: a toolkit to summarize, annotate and visualize genomic intervals.

2015-04 | Journal article
DOI:

10.1093/bioinformatics/btu775

PMID:

25417204

Contributors: Akalin A; Franke V; Vlahoviček K; Mason CE; Schübeler D
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells.

2014 | Journal article
DOI:

10.1371/journal.pone.0092689

PMID:

24658136

PMC:

PMC3962432

Contributors: Yukawa M; Akiyama T; Franke V; Mise N; Isagawa T; Suzuki Y; Suzuki MG; Vlahovicek K; Abe K; Aburatani H et al.
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs.

2014-04 | Journal article
DOI:

10.1093/nar/gku164

PMID:

24569352

PMC:

PMC4005694

Contributors: Godinic-Mikulcic V; Jaric J; Greber BJ; Franke V; Hodnik V; Anderluh G; Ban N; Weygand-Durasevic I
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

A cohesin-independent role for NIPBL at promoters provides insights in CdLS.

2014-02 | Journal article
DOI:

10.1371/journal.pgen.1004153

PMID:

24550742

PMC:

PMC3923681

Contributors: Zuin J; Franke V; van Ijcken WF; van der Sloot A; Krantz ID; van der Reijden MI; Nakato R; Lenhard B; Wendt KS
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes.

2013-11 | Journal article
DOI:

10.1016/j.cell.2013.10.001

PMID:

24209619

Contributors: Flemr M; Malik R; Franke V; Nejepinska J; Sedlacek R; Vlahovicek K; Svoboda P
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

Prediction of interacting protein residues using sequence and structure data.

2012 | Journal article
DOI:

10.1007/978-1-61779-465-0_16

PMID:

22183541

Contributors: Franke V; Sikić M; Vlahoviček K
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

The male germ cell gene regulator CTCFL is functionally different from CTCF and binds CTCF-like consensus sites in a nucleosome composition-dependent manner.

2012 | Journal article
DOI:

10.1186/1756-8935-5-8

PMID:

22709888

PMC:

PMC3418201

Contributors: Sleutels F; Soochit W; Bartkuhn M; Heath H; Dienstbach S; Bergmaier P; Franke V; Rosa-Garrido M; van de Nobelen S; Caesar L et al.
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

A novel complex, RUNX1-MYEF2, represses hematopoietic genes in erythroid cells.

2012-10 | Journal article
DOI:

10.1128/MCB.05938-11

PMID:

22801375

PMC:

PMC3457535

Contributors: van Riel B; Pakozdi T; Brouwer R; Monteiro R; Tuladhar K; Franke V; Bryne JC; Jorna R; Rijkers EJ; van Ijcken W et al.
Source: Self-asserted source
Vedran Franke via Europe PubMed Central

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

2012-06 | Journal article
DOI:

10.1002/0471250953.bi1109s38

PMID:

22700313

PMC:

PMC3412548

Contributors: Afgan E; Chapman B; Jadan M; Franke V; Taylor J
Source: Self-asserted source
Vedran Franke via Europe PubMed Central