• Gene Regulatory Adaptation to Darkness Across Cavefish Development - CaveAGE

  26.10.2026 - 25.10.2029 | 199,870.00 EUR

  CroRISIRB

• PROSPER: PROmoter Structure and Protist Evolutionary Resilience - PROSPER

  01.01.2025 - 31.12.2027 | 150,000.00 EUR

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• Addressing copper pollution in South Europe by robustifying whole-cell copper biosensors through cell wall engineering - robustiCo

  09.12.2024 - 08.12.2027 | 200,000.00 EUR

  CroRIS

• DANIO-CODE - the next frontier: Decoding transcription regulation in regeneration by advanced genomics and computational tools - DANIO-ReCODE

  01.11.2024 - 31.10.2028 | 2,785,636.80 EUR

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• Introducing cap analysis of gene expression (CAGE) to the Croatian research systemas a scaffold for finding anti-tumour targets - CroAGE

  01.07.2023 - 31.07.2026 | 748,061.25 EUR

  CroRISIRB

Original scientific paper

• Phan, Mai H. Q.; Zehnder, Tobias; Puntieri, Fiona; Magg, Andreas; Majchrzycka, Blanka; Antonović, Milan; Wieler, Hannah; Lo, Bai-Wei; Baranašić, Damir; Lenhard, Boris et al. | Conservation of regulatory elements with highly diverged sequences across large evolutionary distances // Nature genetics, 57 (2025), 6; 1524-1534. doi: 10.1038/s41588-025-02202-5

  doiwww.nature.comfulir.irb.hr

• Amblard, Irène; Baranašić, Damir; Xie, Sheila Q.; Moyon, Benjamin; Percharde, Michelle; Lenhard, Boris; Metzis, Vicki | A dual enhancer-attenuator element ensures transient Cdx2 expression during mouse posterior body formation // Developmental cell, 60 (2025), 18; 2407-2419.e6. doi: 10.1016/j.devcel.2025.06.006

  doiwww.cell.comwww.sciencedirect.comfulir.irb.hr

• Ovek Baydar, Damla; Rauluseviciute, Ieva; Aronsen, Dina R; Blanc-Mathieu, Romain; Bonthuis, Ine; de Beukelaer, Herman; Ferenc, Katalin; Jegou, Alice; Kumar, Vipin; Lemma, Roza Berhanu et al. | JASPAR 2026: expansion of transcription factor binding profiles and integration of deep learning models // Nucleic acids research, 54 (2025), D1; D184-D193. doi: 10.1093/nar/gkaf1209

  doifulir.irb.hracademic.oup.com

• Naseer, Shahmir; Clark, Thomas C; Collet, Bertrand; Dewari, Pooran; Baranašić, Damir; Macqueen, Daniel J; Boudinot, Pierre; Martin, Samuel A.M. | Genomic regulatory landscape underlying the antiviral response of Atlantic salmon // Genome research, -36 (2025), 8; 1-47. doi: 10.1101/gr.280579.125

  doifulir.irb.hrgenome.cshlp.org

• Miranda, Antonio M. A.; McAllan, Liam; Mazzei, Guianfranco; Andrew, Ivan; Davies, Iona; Ertugrul, Meryem; Kenkre, Julia; Kudo, Hiromi; Carrelha, Joana; Patel, Bhavik et al. | Selective remodelling of the adipose niche in obesity and weight loss // Nature, 644 (2025), 8077; 769-779. doi: 10.1038/s41586-025-09233-2

  doifulir.irb.hrwww.nature.com

• Rauluseviciute, Ieva; Riudavets-Puig, Rafael; Blanc-Mathieu, Romain; Castro-Mondragon, Jaime A; Ferenc, Katalin; Kumar, Vipin; Lemma, Roza Berhanu; Lucas, Jérémy; Chèneby, Jeanne; Baranasic, Damir et al. | JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles // Nucleic acids research, 52 (2023), D1; D174-D182. doi: 10.1093/nar/gkad1059

  doiacademic.oup.comfulir.irb.hr

• McAllan, Liam; Baranasic, Damir; Villicaña, Sergio; Brown, Scarlett; Zhang, Weihua; Lehne, Benjamin; Adamo, Marco; Jenkinson, Andrew; Elkalaawy, Mohamed; Mohammadi, Borzoueh et al. | Integrative genomic analyses in adipocytes implicate DNA methylation in human obesity and diabetes // Nature communications, 14 (2023), 1; 2784, 20. doi: 10.1038/s41467-023-38439-z

  doiwww.nature.comwww.nature.com

• Baranasic, Damir; Hörtenhuber, Matthias; Balwierz, Piotr J.; Zehnder, Tobias; Mukarram, Abdul Kadir; Nepal, Chirag; Várnai, Csilla; Hadzhiev, Yavor; Jimenez-Gonzalez, Ada; Li, Nan et al. | Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements // Nature genetics, 54 (2022), 7; 1037-1050. doi: 10.1038/s41588-022-01089-w

  doiwww.nature.comwww.nature.com

• Slemc, Lucija; Jakše, Jernej; Filisetti, Alessandro; Baranasic, Damir; Rodríguez-García, Antonio; Del Carratore, Francesco; Marino, Stefano Maria; Zucko, Jurica; Starcevic, Antonio; Šala, Martin et al. | Reference-Grade Genome and Large Linear Plasmid of Streptomyces rimosus: Pushing the Limits of Nanopore Sequencing // Microbiology spectrum, 10 (2022), 2; e02434-21, 20. doi: 10.1128/spectrum.02434-21

  doijournals.asm.orgjournals.asm.org

• Castro-Mondragon, Jaime A; Riudavets-Puig, Rafael; Rauluseviciute, Ieva; Berhanu Lemma, Roza; Turchi, Laura; Blanc-Mathieu, Romain; Lucas, Jeremy; Boddie, Paul; Khan, Aziz; Manosalva Pérez, Nicolás et al. | JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles // Nucleic acids research, 50 (2021), D1; D165-D173. doi: 10.1093/nar/gkab1113

  doiacademic.oup.comacademic.oup.com

• Fornes, Oriol; Castro-Mondragon, Jaime A; Khan, Aziz; van der Lee, Robin; Zhang, Xi; Richmond, Phillip A; Modi, Bhavi P; Correard, Solenne; Gheorghe, Marius; Baranašić, Damir et al. | JASPAR 2020: update of the open-access database of transcription factor binding profiles // Nucleic acids research, 48 (2019), D1; D87-D92. doi: 10.1093/nar/gkz1001

  doiacademic.oup.comacademic.oup.com

• Khan, Aziz; Fornes, Oriol; Stigliani, Arnaud; Gheorghe, Marius; Castro-Mondragon, Jaime A; van der Lee, Robin; Bessy, Adrien; Chèneby, Jeanne; Kulkarni, Shubhada R; Tan, Ge et al. | JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework // Nucleic acids research, 46 (2017), D1; D1284-D1284. doi: 10.1093/nar/gkx1188

  doi

• Baranasic, Damir; Oppermann, Timo; Cheaib, Miriam; Cullum, John; Schmidt, Helmut; Simon, Martin | Genomic Characterization of Variable Surface Antigens Reveals a Telomere Position Effect as a Prerequisite for RNA Interference-Mediated Silencing in <i>Paramecium tetraurelia</i> // mBio, 5 (2014), 6; e01328-14, 16. doi: 10.1128/mbio.01328-14

  doi

• Baranašić, Damir ; Zucko, Jurica ; Diminic, Janko ; Gacesa, Ranko ; Long, F Paul ; Cullum, John ; Hranueli, Daslav ; Starcevic, Antonio | Prediction of the substrate specificity of adenylation domains of non-ribosomal peptide synthetases and other protein properties by latent semantic indexing // Journal of industrial microbiology & biotechnology, 41 (2013), 2; 461-467. doi: 10.1007/s10295-013-1322-2

  doi

• Blažić, Marko ; Starčević, Antonio ; Lisfi, Mohamed ; Baranašić, Damir ; Goranovič, Dušan ; Fujs, Štefan ; Kuščer, Enej ; Kosec, Gregor ; Petković, Hrvoje ; Cullum, John et al. | Annotation of the modular polyketide synthase and nonribosomal peptide synthetase gene clusters in the genome of Streptomyces tsukubaensis NRRL18488 // Applied and environmental microbiology, 78 (2012), 23; 8183-8190. doi: 10.1128/AEM.01891-12

  doiaem.asm.orgaem.asm.org

Review, commentary, critique

• Jimenez Gonzalez, Ada; Baranasic, Damir; Müller, Ferenc | Zebrafish regulatory genomic resources for disease modelling and regeneration // Disease Models & Mechanisms, 16 (2023), 8; dmm050280, 10. doi: 10.1242/dmm.050280

  doijournals.biologists.comfulir.irb.hr

Conference abstract

• Žunar, Bojan; Baranašić, Damir; Paić, Antonia; Lenhard, Boris | Predicting conserved promoter strength across the Saccharomyces clade: a comparative CAGE resource for fungal strain engineering // PYFF9 Programme and Abstract Book. | EFB Microbial Biotechnology, 2026. str. 282-282

• Kajan, Katarina; Žunar, Bojan; Johnston, Alex; Trejo-Reveles, Violeta; Libby, Ashley; Briscoe, James; Meddle, Simone; Lenhard, Boris; Baranašić, Damir | Comparative analysis of transcription initialisation principles in early avian development // ISMB/ECCB 2025 : Book of Abstracts / International Society for Computational Biology (ur.). | International Society for Computational Biology, 2025. str. 897-898

  www.iscb.org

• Bošnjaković, Marta; Guan, Qianhong; Otten, Cecile Francoise Eleonore; Popović, Marta; Žunar, Bojan; Mueller, Ferenc; Lenhard, Boris; Baranašić, Damir | Expanding DANIO - CODE: The base pair identification of promoters across adult zebrafish organs // ISMB/ECCB 2025 : Book of Abstracts / International Society for Computational Biology (ur.). | International Society for Computational Biology, 2025. str. 815-816

  www.iscb.org

• Zou, Xinchen; Lenhard, Boris; Baranašić, Damir; de Mendoza, Alex; Xu, Lan; Žunar, Bojan | Concerted evolution of functional promoter classes in Metazoa: comparative insights into promoter architecture // Scientific Meeting Transcription and Chromatin UK Abstract Book. | The Company of Biologists, 2025

• Gómez-Marín, Elena; Žunar, Bojan; Kaur, Ekjot; D'Orazio, Fabio; Baranašić, Damir; R. Barr, Alexis; Lenhard, Boris | Promoter activity and transcript stability dynamics reveal regulatory principles of cell cycle–dependent transcription // Scientific Meeting Transcription and Chromatin UK Abstract Book. | The Company of Biologists, 2025

• Kajan, Katarina; Baranašić, Damir | Biophysical properties of transcription initiation during embryonic development // 1st Meeting of Young Biophysicists: Programme & Book of Abstracts / Kutnjak, Marin; Inkret, Suzana; Vujica, Lana et al. (ur.). | Zagreb: Croatian Biophysical Society, Ruđer Bošković Institute, 2025. str. 14-14

• Bošnjaković Marta; Kajan Katarina; Piškorec Matija; Baranašić Damir | CAGEflow – programski tok za analizu visokoprotočnih podataka dobivenih CAGE sekvenciranjem // Dani e-infrastrukture Srce DEI 2025: knjiga sažetaka / Mihaljević, Slaven; Veldić, Ivana (ur.). | Zagreb: SRCE, 2025. str. 56-56

• Renko, Ira; Sidorov, Sviatoslav; Ferenc, Katalin Terezia; Kajan, Katarina; Bošnjakovic, Marta; Mathelier, Anthony; Lenhard, Boris; Baranašić, Damir | Rebuilding the Zebrafish Promoter Atlas: A Reproducible and Scalable Reanalysis of DANIOCODE CAGE Data Using CAGEflow // ISMB/ECCB 2025 : Book of Abstracts / International Society for Computational Biology (ur.). | International Society for Computational Biology, 2025. str. 88-88

• Bošnjaković Marta; Guan Qianhong; Francoise Eleonore Otten Cecile; Popović Marta; Žunar Bojan; Mueller Ferenc; Lenhard Boris; Baranašić Damir | Karakterizacija promotorskih regija u zebrici (Danio rerio) korištenjem analize ekspresije RNA s 5'-GTP-kapom // ZBORNIK SAŽETAKA: Dani doktorata biotehničkog područja 2025. / Novak, Jasna; Beljo Lučić, Ružica; Širić, Ivan et al. (ur.). | Zagreb: Sveučilište u Zagrebu Prehrambeno-biotehnološki fakultet, 2025. str. 47-47

• Bošnjaković Marta; Baranašić Damir | High-resolution mapping of transcription start sites using CAGE-seq // 1st Meeting of Young Biophysicists: Programme & Book of Abstracts / Kutnjak, Marin; Inkret, Suzana; Vujica, Lana et al. (ur.). | Zagreb: Croatian Biophysical Society, Ruđer Bošković Institute, 2025. str. 15-15

• Baranašić, Damir; Žunar, Bojan; Bošnjaković, Marta; Jimenez-Gonzalez, Ada; Hadzhiev, Javor; Müller, Ferenc; Lenhard, Boris | FUNCTIONAL IMPACTS OF PROMOTER EVOLUTION IN Cyprinus carpio carpio REVEALED BY HIGH-RESOLUTION CAGE ANALYSIS // FEBS3+ Meeting: Exploring Molecular Frontiers / Dulić, Morana; Sinčić, Nino; Stuparević, Igor (ur.). | Zagreb: Hrvatsko društvo za biokemiju i molekularnu biologiju, 2024. str. 87-87

• Gómez-Marín, Elena; Žunar, Bojan; Kaur, Ekjot; D'Orazio, Fabio; Baranašić, Damir; R. Barr, Alexis; Lenhard, Boris | MONITORING THE CELL CYCLE DYNAMICS OF PROMOTER ACTIVITY WITH NET-SLIC-CAGE REVEALS NOVEL RULES OF CELL CYCLE STAGE-SPECIFIC TRANSCRIPTIONAL REGULATION // FEBS3+ Meeting: Exploring Molecular Frontiers / Dulić, Morana; Sinčić, Nino; Stuparević, Igor (ur.). | Zagreb: Hrvatsko društvo za biokemiju i molekularnu biologiju, 2024. str. 117-117

• Bošnjaković Marta; Žunar Bojan; Bilandžija Helena; Lenhard Boris; Baranašić Damir | Analysis of transcription initiation in early embryonic development of the surface and cave forms of Astyanax mexicanus highlight regulatory rules of harsh environment adaptation. // Transcription and chromatin / The European Molecular Biology Laboratory (ur.). | Heidelberg: The European Molecular Biology Laboratory, 2024. str. 107-107

Unpublished conference paper

• Marta Bošnjaković, Bojan Žunar, Helena Bilandžija, Boris Lenhard, Damir Baranašić | Analysis of transcription initiation in early embryonic development of the surface and cave forms of Astyanax mexicanus // Awakening the Genome During Developmental Reprogramming: From Embryos to Organoids (EMBO Workshop) | Sevilla, Španjolska, 04.05.2026-07.05.2026

• Marta Bošnjaković, Qianhong Guan, Cecile Francoise Eleonore Otten, Marta Popović, Bojan Žunar, Boris Lenhard, Ferenc Mueller, Damir Baranašić | Promoter-level annotation of the adult zebrafish regulatory landscape using CAGE-seq // 1st German Fish Meeting | Heidelberg, Njemačka, 16.09.2026-18.09.2026

• Paić, Antonia; Baranašić, Damir; Martinić Cezar, Tea; Vuraić, Kristijan; Teparić, Renata; Vallée, Béatrice; Žunar, Bojan | Exploring cell wall diversity in S. cerevisiae identifies new candidate strains for robust bioengineering // FEBS3+ Meeting: Unlocking of the Secrets of Life | Prag, Češka Republika, 07.09.2025-10.09.2025

• Žunar, Bojan; Paić, Antonia; Vallée, Béatrice; Baranašić, Damir | Beta-glucan exposé: quantifying the diversity of yeast cell wall // Woodstock.Bio2 + Night Science | Prag, Češka Republika, 10.06.2025-13.06.2025

• Žunar, Bojan; Franić, Dina; Paić, Antonia; Vuraić, Kristijan; Baranašić, Damir | Expanding the promoter toolbox: using promoters from Saccharomyces sister species to drive gene expression in Saccharomyces cerevisiae // 38th International Specialized Symposium on Yeasts (ISSY38) - Yeast – the Omni-Tool | Varšava, Poljska, 01.09.2025-05.09.2025

• Žunar, Bojan; Baranašić, Damir; Paić, Antonia; Lenhard, Boris | Comparative CAGE Analysis Reveals 20 Million Years of Yeast Promoter Evolution // Cold Spring Harbor Laboratory Conference on Genome Informatics | Cold Spring Harbor (NY), Sjedinjene Američke Države, 05.11.2025-08.11.2025

• Kajan, Katarina; Žunar, Bojan; Johnston, Alex; Trejo-Reveles, Violeta; Libby, Ashley; Briscoe, James; Meddle, Simone; Lenhard, Boris; Baranašić, Damir | Promoter architecture and transcriptional activity during early avian embryonic development // Cold Spring Harbor Laboratory Conference on Mechanisms of Eukaryotic Transcription | Cold Spring Harbor (NY), Sjedinjene Američke Države, 26.08.2025-30.08.2025

• Bošnjaković Marta; Guan Qianhong; Otten Cecile Francoise Eleonore; Popović Marta; Žunar Bojan; Mueller Ferenc; Lenhard Boris; Baranašić Damir | Validation of chromatin-annotated cis-regulatory elements using CAGE-seq in adult zebrafish tissues // Cold Spring Harbor Laboratory Conference on Mechanisms of Eukaryotic Transcription | Cold Spring Harbor (NY), Sjedinjene Američke Države, 26.08.2025-30.08.2025