Journal Article
M. Migdał, Arakawa, T., Takizawa, S., Furuno, M., Suzuki, H., Arner, E., Winata, C. Lanny, and Kaczkowski, B.,
“xcore: an R package for inference of gene expression regulators.”,
BMC Bioinformatics, vol. 24, no. 1, p. 14, 2023.
R. Minhas, Paterek, A., Łapiński, M., Bazała, M., Korzh, V., and Winata, C. L.,
“A novel conserved enhancer at zebrafish zic3 and zic6 loci drives neural expression.”,
Dev Dyn, vol. 248, no. 9, pp. 837-849, 2019.
H. Aanes, Winata, C. L., Lin, C. Ho, Chen, J. P., Srinivasan, K. G., Lee, S. G. P., Lim, A. Y. M., Hajan, H. Shreen, Collas, P., Bourque, G., Gong, Z., Korzh, V., Aleström, P., and Mathavan, S.,
“Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition.”,
Genome Res, vol. 21, no. 8, pp. 1328-38, 2011.
R. Minhas, Loeffler-Wirth, H., Siddiqui, Y. H., Obrębski, T., Vashisht, S., Nahia, K. Abu, Paterek, A., Brzozowska, A., Bugajski, L., Piwocka, K., Korzh, V., Binder, H., and Winata, C. Lanny,
“Transcriptome profile of the sinoatrial ring reveals conserved and novel genetic programs of the zebrafish pacemaker.”,
BMC Genomics, vol. 22, no. 1, p. 715, 2021.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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