Preprint Loss of Brg1 promotes seizure development via GABAergic system disruption. Pagano R, Abu Nahia K, Declève A, Stadnik D, Zmorzyńska J, A. Serwa RA, Copmans D, Jaworski J. bioRxiv. 2026 Preprint Enhancer-mediated metabolic pre-patterning defines trabecular cardiomyocyte identity prior to morphogenesis. Parisi C, Vashisht S, Nasab MSG, Kandhadayar SG, Misztal K, Zagorski M, Winata C. bioRxiv. 2026 Publication Zebrafish as a model for Catel-Manzke syndrome-identification and characterization of the zebrafish TGDS ortholog. Coppola MR, Bellitto D, Asgari E, Bazzurro V, Casucci G, Piacente F, Bozzo M, Ceresa D, Parisi C, Winata C, Candiani S, Tonetti M. FEBS J. 2025 Publication Epigenomics and transcriptomics profiles of developing zebrafish heart cells. Chahal G, Eichenlaub MP, Tondl M, Pawlak M, Mohenska M, Grimm L, Bottrell L, Drvodelic M, Alaei S, Hallab J, Waylen LN, Polo JM, Blanpain C, Palpant N, Rossello FJ, Änkö ML, Currie PD, Hogan BM, Winata C, Salimova E, Nim HT, Ramialison M. Sci Data. 2025 Publication Protocol for the preparation of zebrafish whole heart cell suspension for single-cell analyses. Abu Nahia K, Winata CL. STAR Protoc. 2025 Publication Computational analysis of congenital heart disease associated SNPs: unveiling their impact on the gene regulatory system. Vashisht S, Parisi C, Winata CL. BMC Genomics. 2025 Preprint Computational analysis of congenital heart disease associated SNPs: Unveiling their impact on the gene regulatory system. Vashisht S, Parisi C, Winata CL. medRxiv. 2024 Publication scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation. Abu Nahia K, Sulej A, Migdał M, Ochocka N, Ho R, Kamińska B, Zagorski M, Winata CL. iScience. 2024 Publication Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish. Uszczynska-Ratajczak B, Sugunan S, Kwiatkowska M, Migdal M, Carbonell-Sala S, Sokol A, Winata CL, Chacinska A. Life Sci Alliance. 2023 Publication xcore: an R package for inference of gene expression regulators. Migdał M, Arakawa T, Takizawa S, Furuno M, Suzuki H, Arner E, Winata CL, Kaczkowski B. BMC Bioinformatics.. 2023 Publication A Zebrafish/Drosophila Dual System Model for Investigating Human Microcephaly. Bartoszewski S, Dawidziuk M, Kasica N, Durak R, Jurek M, Podwysocka A, Guilbride DL, Podlasz P, Winata CL, Gawlinski PA. Cells. 2022 Publication Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Nat Genet. 2022 Publication Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish. Niescierowicz K#, Pryszcz L#, Navarrete C#, Tralle E#, Sulej A#, Abu Nahia K, Kasprzyk ME, Misztal K, Pateria A, Pakuła A, Bochtler M, Winata C. ^# Contributed equally Nat Commun. 2022 Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift. Migdał M, Tralle E, Abu Nahia K, Bugajski Ł, Kędzierska KZ, Garbicz F, Piwocka K, Winata CL, Pawlak M. BMC Genomics.. 2021 Transcriptome profile of the sinoatrial ring reveals conserved and novel genetic programs of the zebrafish pacemaker. Minhas R, Loeffler-Wirth H, Siddiqui YH, Obrębski T, Vashisht S, Abu Nahia K, Paterek A, Brzozowska A, Bugajski L, Piwocka K, Korzh V, Binder H, Winata CL. BMC Genomics.. 2021 Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region. Abu Nahia K, Migdał M, Quinn TA, Poon KL, Łapiński M, Sulej A, Liu J, Mondal SS, Pawlak M, Bugajski Ł, Piwocka K, Brand T, Kohl P, Korzh V, Winata C. Cell Mol Life Sci.. 2021 Cardiac-specific β-catenin deletion dysregulates energetic metabolism and mitochondrial function in perinatal cardiomyocytes. Balatskyi VV, Vaskivskyi VO, Myronova A, Avramets D, Nahia KA, Macewicz LL, Ruban TP, Kucherenko DY, Soldatkin OO, Lushnikova IV, Skibo GG, Winata CL, Dobrzyn P, Piven OO. Mitochondrion.. 2021 The development of zebrafish pancreas affected by deficiency of Hedgehog signaling. Korzh S, Winata CL, Gong Z, Korzh V. Gene Expr Patterns.. 2021 Fish-Ing for Enhancers in the Heart. Parisi C, Vashisht S, Winata CL. J Mol Sci.. 2021 Exploring Translational Control of Maternal mRNAs in Zebrafish. Winata  CL, Łapiński  M, Ismail  H, Mathavan  S, Sampath P. Methods Mol Biol.. 2021 The zebrafish as a model for developmental and biomedical research in Poland and beyond. Winata CL, Dodzian J, Bialek-Wyrzykowska U. Dev Biol.. 2020 Targeted RNA Knockdown by a Type III CRISPR-Cas Complex in Zebrafish. Fricke T, Smalakyte D, Lapinski M, Pateria A, Weige C, Pastor M, Kolano A, Winata C, Siksnys V, Tamulaitis G, Bochtler M. CRISPR J.. 2020 MetaPhOrs 2.0: Integrative, Phylogeny-Based Inference of Orthology and Paralogy Across the Tree of Life. Chorostecki U, Molina M, Pryszcz LP, Gabaldón T. Nucleic Acids Res.. 2020 MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets Cozzuto L, Liu H, Pryszcz LP, Pulido TH, Delgado-Tejedor A, Ponomarenko J, Novoa EM. Front Genet.. 2020 A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression. Minhas R, Paterek A, Łapiński M, Bazała M, Korzh V, Winata CL Dev Dyn. . 2019 Interplay of Chimeric Mating-Type Loci Impairs Fertility Rescue and Accounts for Intra-Strain Variability in Zygosaccharomyces rouxii Interspecies Hybrid ATCC42981. Bizzarri M, Cassanelli S, Bartolini L, Pryszcz LP, Dušková M, Sychrová H, Solieri L. Front Genet.. 2019 Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination. Pawełkowicz M, Pryszcz L, Skarzyńska A, Wóycicki RK, Posyniak K, Rymuszka J, Przybecki Z, Pląder W. Plant Reprod. . 2019 Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development. Pawlak M, Kedzierska KZ, Migdal M, Nahia KA, Ramilowski JA, Bugajski L, Hashimoto K, Marconi A, Piwocka K, Carninci P, Winata CL. Genome Res.. 2019 Draft Genome Sequences of the Highly Halotolerant Strain Zygosaccharomyces rouxii ATCC 42981 and the Novel Allodiploid Strain Zygosaccharomyces sapae ATB301T Obtained Using the MinION Platform. Bizzarri M, Cassanelli S, Pryszcz LP, Gawor J, Gromadka R, Solieri L. Microbiol Resour Announc.. 2018 nextPARS: parallel probing of RNA structures in Illumina. Saus E, Willis JR, Pryszcz LP, Hafez A, Llorens C, Himmelbauer H, Gabaldón T. RNA. 2018