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A
K. Niescierowicz, Pryszcz, L., Navarrete, C., Tralle, E., Sulej, A., Nahia, K. Abu, Kasprzyk, M. Elżbieta, Misztal, K., Pateria, A., Pakuła, A., Bochtler, M., and Winata, C., “Adar-mediated A-to-I editing is required for embryonic patterning and innate immune response regulation in zebrafish.”, Nat Commun, vol. 13, no. 1, p. 5520, 2022.
C
V. V. Balatskyi, Vaskivskyi, V. O., Myronova, A., Avramets, D., Nahia, K. Abu, Macewicz, L. L., Ruban, T. P., Kucherenko, D. 'yaYu, Soldatkin, O. O., Lushnikova, I. V., Skibo, G. G., Winata, C. L., Dobrzyn, P., and Piven, O. O., “Cardiac-specific β-catenin deletion dysregulates energetic metabolism and mitochondrial function in perinatal cardiomyocytes.”, Mitochondrion, vol. 60, pp. 59-69, 2021.
V. V. Balatskyi, Vaskivskyi, V. O., Myronova, A., Avramets, D., Nahia, K. Abu, Macewicz, L. L., Ruban, T. P., Kucherenko, D. 'yaYu, Soldatkin, O. O., Lushnikova, I. V., Skibo, G. G., Winata, C. L., Dobrzyn, P., and Piven, O. O., “Cardiac-specific β-catenin deletion dysregulates energetic metabolism and mitochondrial function in perinatal cardiomyocytes.”, Mitochondrion, vol. 60, pp. 59-69, 2021.
L. C. Lindeman, Winata, C. L., Aanes, H., Mathavan, S., Alestrom, P., and Collas, P., “Chromatin states of developmentally-regulated genes revealed by DNA and histone methylation patterns in zebrafish embryos.”, Int J Dev Biol, vol. 54, no. 5, pp. 803-13, 2010.
C. L. Winata, Łapiński, M., Pryszcz, L., Vaz, C., Bin Ismail, M. H., Nama, S., Hajan, H. S., Lee, S. G. P., Korzh, V., Sampath, P., Tanavde, V., and Mathavan, S., “Cytoplasmic polyadenylation-mediated translational control of maternal mRNAs directs maternal-to-zygotic transition”, Development, vol. 145, 2018.
D
M. Pawlak, Kedzierska, K. Z., Migdal, M., Nahia, K. Abu, Ramilowski, J. A., Bugajski, L., Hashimoto, K., Marconi, A., Piwocka, K., Carninci, P., and Winata, C. L., “Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development.”, Genome Res, vol. 29, no. 3, pp. 506-519, 2019.
M. Pawlak, Kedzierska, K. Z., Migdal, M., Nahia, K. Abu, Ramilowski, J. A., Bugajski, L., Hashimoto, K., Marconi, A., Piwocka, K., Carninci, P., and Winata, C. L., “Dynamics of cardiomyocyte transcriptome and chromatin landscape demarcates key events of heart development.”, Genome Res, vol. 29, no. 3, pp. 506-519, 2019.
E
C. Lanny Winata, Łapiński, M., Ismail, H., Mathavan, S., and Sampath, P., “Exploring Translational Control of Maternal mRNAs in Zebrafish.”, Methods Mol Biol, vol. 2218, pp. 367-380, 2021.
G
C. L. Winata, Kondrychyn, I., Kumar, V., Srinivasan, K. G., Orlov, Y., Ravishankar, A., Prabhakar, S., Stanton, L. W., Korzh, V., and Mathavan, S., “Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish.”, PLoS Genet, vol. 9, no. 10, p. e1003852, 2013.
K. Abu Nahia, Migdał, M., T Quinn, A., Poon, K. - L., Łapiński, M., Sulej, A., Liu, J., Mondal, S. S., Pawlak, M., Bugajski, Ł., Piwocka, K., Brand, T., Kohl, P., Korzh, V., and Winata, C., “Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region.”, Cell Mol Life Sci, vol. 78, no. 19-20, pp. 6669-6687, 2021.
K. Abu Nahia, Migdał, M., T Quinn, A., Poon, K. - L., Łapiński, M., Sulej, A., Liu, J., Mondal, S. S., Pawlak, M., Bugajski, Ł., Piwocka, K., Brand, T., Kohl, P., Korzh, V., and Winata, C., “Genomic and physiological analyses of the zebrafish atrioventricular canal reveal molecular building blocks of the secondary pacemaker region.”, Cell Mol Life Sci, vol. 78, no. 19-20, pp. 6669-6687, 2021.
I
K. Hana Utami, Winata, C. L., Hillmer, A. M., Aksoy, I., Long, H. Truong, Liany, H., G Y Chew, E., Mathavan, S., Tay, S. K. H., Korzh, V., Sarda, P., Davila, S., and Cacheux, V., “Impaired development of neural-crest cell-derived organs and intellectual disability caused by MED13L haploinsufficiency.”, Hum Mutat, vol. 35, no. 11, pp. 1311-20, 2014.
M
C. Yong Ung, Lam, S. Hong, Hlaing, M. Myintzu, Winata, C. L., Korzh, S., Mathavan, S., and Gong, Z., “Mercury-induced hepatotoxicity in zebrafish: in vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation.”, BMC Genomics, vol. 11, p. 212, 2010.
D. Baranasic, Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. Kadir, Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F. M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S. E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A. C., Kopp, W., Chambers, E., Wang, D., Kim, H. R., Acemel, R. D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S. Allen, Burgess, S. M., Winata, C., van Eeden, F., Vaquerizas, J. M., Gómez-Skarmeta, J. Luis, Onichtchouk, D., Brown, B. James, Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F. C., Daub, C. O., Lenhard, B., and Müller, F., “Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.”, Nat Genet, vol. 54, no. 7, pp. 1037-1050, 2022.
D. Baranasic, Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. Kadir, Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F. M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S. E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A. C., Kopp, W., Chambers, E., Wang, D., Kim, H. R., Acemel, R. D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S. Allen, Burgess, S. M., Winata, C., van Eeden, F., Vaquerizas, J. M., Gómez-Skarmeta, J. Luis, Onichtchouk, D., Brown, B. James, Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F. C., Daub, C. O., Lenhard, B., and Müller, F., “Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.”, Nat Genet, vol. 54, no. 7, pp. 1037-1050, 2022.
D. Baranasic, Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. Kadir, Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F. M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S. E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A. C., Kopp, W., Chambers, E., Wang, D., Kim, H. R., Acemel, R. D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S. Allen, Burgess, S. M., Winata, C., van Eeden, F., Vaquerizas, J. M., Gómez-Skarmeta, J. Luis, Onichtchouk, D., Brown, B. James, Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F. C., Daub, C. O., Lenhard, B., and Müller, F., “Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.”, Nat Genet, vol. 54, no. 7, pp. 1037-1050, 2022.
D. Baranasic, Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. Kadir, Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F. M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S. E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A. C., Kopp, W., Chambers, E., Wang, D., Kim, H. R., Acemel, R. D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S. Allen, Burgess, S. M., Winata, C., van Eeden, F., Vaquerizas, J. M., Gómez-Skarmeta, J. Luis, Onichtchouk, D., Brown, B. James, Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F. C., Daub, C. O., Lenhard, B., and Müller, F., “Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.”, Nat Genet, vol. 54, no. 7, pp. 1037-1050, 2022.
D. Baranasic, Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. Kadir, Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., Wragg, J., D'Orazio, F. M., Relic, D., Pachkov, M., Díaz, N., Hernández-Rodríguez, B., Chen, Z., Stoiber, M., Dong, M., Stevens, I., Ross, S. E., Eagle, A., Martin, R., Obasaju, O., Rastegar, S., McGarvey, A. C., Kopp, W., Chambers, E., Wang, D., Kim, H. R., Acemel, R. D., Naranjo, S., Łapiński, M., Chong, V., Mathavan, S., Peers, B., Sauka-Spengler, T., Vingron, M., Carninci, P., Ohler, U., Lacadie, S. Allen, Burgess, S. M., Winata, C., van Eeden, F., Vaquerizas, J. M., Gómez-Skarmeta, J. Luis, Onichtchouk, D., Brown, B. James, Bogdanovic, O., van Nimwegen, E., Westerfield, M., Wardle, F. C., Daub, C. O., Lenhard, B., and Müller, F., “Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.”, Nat Genet, vol. 54, no. 7, pp. 1037-1050, 2022.
M. Migdał, Tralle, E., Nahia, K. Abu, Bugajski, Ł., Kędzierska, K. Zofia, Garbicz, F., Piwocka, K., Winata, C. Lanny, and Pawlak, M., “Multi-omics analyses of early liver injury reveals cell-type-specific transcriptional and epigenomic shift.”, BMC Genomics, vol. 22, no. 1, p. 904, 2021.
N
H. Aanes, Winata, C. L., Moen, L. F., Østrup, O., Mathavan, S., Collas, P., Rognes, T., and Aleström, P., “Normalization of RNA-sequencing data from samples with varying mRNA levels.”, PLoS One, vol. 9, no. 2, p. e89158, 2014.
H. Aanes, Winata, C. L., Moen, L. F., Østrup, O., Mathavan, S., Collas, P., Rognes, T., and Aleström, P., “Normalization of RNA-sequencing data from samples with varying mRNA levels.”, PLoS One, vol. 9, no. 2, p. e89158, 2014.
P
L. C. Lindeman, Andersen, I. S., Reiner, A. H., Li, N., Aanes, H., Østrup, O., Winata, C. L., Mathavan, S., Müller, F., Aleström, P., and Collas, P., “Prepatterning of developmental gene expression by modified histones before zygotic genome activation.”, Dev Cell, vol. 21, no. 6, pp. 993-1004, 2011.
L. C. Lindeman, Andersen, I. S., Reiner, A. H., Li, N., Aanes, H., Østrup, O., Winata, C. L., Mathavan, S., Müller, F., Aleström, P., and Collas, P., “Prepatterning of developmental gene expression by modified histones before zygotic genome activation.”, Dev Cell, vol. 21, no. 6, pp. 993-1004, 2011.
B. Uszczynska-Ratajczak, Sugunan, S., Kwiatkowska, M., Migdal, M., Carbonell-Sala, S., Sokol, A., Winata, C. L., and Chacinska, A., “Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish.”, Life Sci Alliance, vol. 6, no. 1, 2023.
T
S. Hong Lam, Winata, C. L., Tong, Y., Korzh, S., San Lim, W., Korzh, V., Spitsbergen, J., Mathavan, S., Miller, L. D., Liu, E. T., and Gong, Z., “Transcriptome kinetics of arsenic-induced adaptive response in zebrafish liver.”, Physiol Genomics, vol. 27, no. 3, pp. 351-61, 2006.

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