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2025
Protocol for the preparation of zebrafish whole heart cell suspension for single-cell analyses.
Abu Nahia K, Winata CL.
STAR Protoc. 2025
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
2024
Computational analysis of congenital heart disease associated SNPs: Unveiling their impact on the gene regulatory system.
Vashisht S, Parisi C, Winata CL.
medRxiv. 2024
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
2023
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
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
2022
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
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
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
2021
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
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
The zebrafish as a model for developmental and biomedical research in Poland and beyond.
Winata CL, Dodzian J, Bialek-Wyrzykowska U.
Dev Biol.. 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
2019
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
2018
Transcriptome Analyses of Mosaic (MSC) Mitochondrial Mutants of Cucumber in a Highly Inbred Nuclear Background.
Mróz TL, Eves-van den Akker S, Bernat A, Skarzyńska A, Pryszcz L, Olberg M, Havey MJ, Bartoszewski G.
G3 . 2018
Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal to zygotic transition.
Winata CL, Łapiński M, Pryszcz L, Vaz C, Bin Ismail MH, Nama S, Hajan HS, Lee SGP, Korzh V, Sampath P, Tanavde V, Mathavan S.
Development.. 2018
Decoding the Heart through Next Generation Sequencing Approaches.
Pawlak M, Niescierowicz K, Winata CL.
Genes (Basel). . 2018
The translational regulation of maternal mRNAs in time and space.
Winata CL, Korzh V.
FEBS Lett. . 2018
Zebrafish Zic Genes Mediate Developmental Signaling.
Winata CL, Korzh V.
Adv Exp Med Biol. . 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
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
2017
The canonical way to make a heart: β-catenin and plakoglobin in heart development and remodeling
Piven OO, Winata CL
Experimental Biology and Medicine. 2017
Personalized genome sequencing coupled with iPSC technology identifies GTDC1 as a gene involved in neurodevelopmental disorders
Aksoy I, Utami KH, Winata CL, Hillmer AM, Rouam SL, Briault S, Davila S, Stanton LW, Cacheux V
Hum Mol Genet. 2017
PPARs PL
Gross B, Pawlak M, Lefebvre P, Staels B.
Nat Rev Endocrinol TEST. 2017
2016
DANIO-CODE: Toward an Encyclopedia of DNA Elements in Zebrafish
Tan H, Onichtchouk D, Winata C
Zebrafish. 2016
2015
Changing Faces of Transcriptional Regulation Reflected by Zic3
Winata CL, Kondrychyn I, Korzh V
Current Genomics. 2015