ZFIN ID: ZDB-LAB-120608-2
Sivasubbu Lab
PI/Director: Sivasubbu, Sridhar
Contact Person: Sivasubbu, Sridhar
Email: sridhar@igib.in
URL: http://www.igib.res.in
Address: Institute of Genomics and Integrative Biology, (Council of Scientific and Industrial Research) Mall Road, Delhi 110007 India
Country: India
Phone:
Fax:
Line Designation: gib


GENOMIC FEATURES ORIGINATING FROM THIS LAB
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STATEMENT OF RESEARCH INTERESTS


LAB MEMBERS


ZEBRAFISH PUBLICATIONS OF LAB MEMBERS
Raja, D.A., Subramaniam, Y., Aggarwal, A., Gotherwal, V., Babu, A., Tanwar, J., Motiani, R.K., Sivasubbu, S., Gokhale, R.S., Natarajan, V.T. (2020) Histone variant dictates fate biasing of neural crest cells to melanocyte lineage. Development (Cambridge, England). 147(5):
Jagtap, U., Sivadas, A., Basu, S., Verma, A., Sivasubbu, S., Scaria, V., Sachidanandan, C. (2019) A Temporal Map of Gene Expression Pattern During Zebrafish Liver Regeneration. Zebrafish. 17(1):1-10
Raja, D.A., Gotherwal, V., Burse, S.A., Subramaniam, Y.J., Sultan, F., Vats, A., Gautam, H., Sharma, B., Sharma, S., Singh, A., Sivasubbu, S., Gokhale, R.S., Natarajan, V.T. (2019) pH-controlled histone acetylation amplifies melanocyte differentiation downstream of MITF. EMBO reports. 21(1):e48333
GUaRDIAN Consortium, Sivasubbu, S., Scaria, V. (2019) Genomics of rare genetic diseases-experiences from India. Human genomics. 14:1
Sharma, D., Sehgal, P., Mathew, S., Vellarikkal, S.K., Singh, A.R., Kapoor, S., Jayarajan, R., Scaria, V., Sivasubbu, S. (2019) A genome-wide map of circular RNAs in adult zebrafish. Scientific Reports. 9:3432
Mathew, S., Sivadas, A., Sehgal, P., Kaushik, K., Vellarikkal, S.K., Scaria, V., Sivasubbu, S. (2019) Methods to Study Long Noncoding RNA Expression and Dynamics in Zebrafish Using RNA Sequencing. Methods in molecular biology (Clifton, N.J.). 1912:77-110
Bhoyar, R.C., Jadhao, A.G., Sabharwal, A., Ranjan, G., Sivasubbu, S., Pinelli, C. (2018) Knockdown of calcium-binding calb2a and calb2b genes indicates the key regulator of the early development of the zebrafish, Danio rerio. Brain structure & function. 224(2):627-642
Ramasamy, S., Sharma, S., Iyengar, B.R., Vellarikkal, S.K., Sivasubbu, S., Maiti, S., Pillai, B. (2018) Identification of novel circadian transcripts in the zebrafish retina. The Journal of experimental biology. 222(Pt 1):
Sabharwal, A., Sharma, D., Vellarikkal, S.K., Jayarajan, R., Verma, A., Senthivel, V., Scaria, V., Sivasubbu, S. (2018) Organellar transcriptome sequencing reveals mitochondrial localization of nuclear encoded transcripts. Mitochondrion. 46:59-68
Nahar, S., Sehgal, P., Azhar, M., Rai, M., Singh, A., Sivasubbu, S., Chakraborty, D., Maiti, S. (2018) A G-quadruplex motif at the 3' end of sgRNAs improves CRISPR-Cas9 based genome editing efficiency. Chemical communications (Cambridge, England). 54(19):2377-2380
Kaushik, K., Sivadas, A., Vellarikkal, S.K., Verma, A., Jayarajan, R., Pandey, S., Sethi, T., Maiti, S., Scaria, V., Sivasubbu, S. (2018) RNA secondary structure profiling in zebrafish reveals unique regulatory features. BMC Genomics. 19:147
Motiani, R.K., Tanwar, J., Raja, D.A., Vashisht, A., Khanna, S., Sharma, S., Srivastava, S., Sivasubbu, S., Natarajan, V.T., Gokhale, R.S. (2018) STIM1 activation of adenylyl cyclase 6 connects Ca2+ and cAMP signaling during melanogenesis.. The EMBO journal. 37(5)
Bhoyar, R.C., Jadhao, A.G., Sivasubbu, S., Singh, A.R., Sabharwal, A., Palande, N.V., Biswas, S. (2017) Neuroanatomical demonstration of calbindin 2a- and calbindin 2b-like calcium binding proteins in the early embryonic development of zebrafish: mRNA study. International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience. 60:26-33
Nathiga Nambi, K.S., Abdul Majeed, S., Taju, G., Sivasubbu, S., Sarath Babu, V., Sahul Hameed, A.S. (2017) Effects of nicotine on zebrafish: a comparative response between a newly established gill cell line and whole gills. Comparative biochemistry and physiology. Toxicology & pharmacology : CBP. 195:68-77
Pawar, N., Gireesh-Babu, P., Sabnis, S., Rasal, K., Murthy, R., Zaidi, S.G., Sivasubbu, S., Chaudhari, A. (2016) Development of a fluorescent transgenic zebrafish biosensor for sensing aquatic heavy metal pollution. Transgenic Research. 25(5):617-27
Singh, A.R., Sivadas, A., Sabharwal, A., Vellarikal, S.K., Jayarajan, R., Verma, A., Kapoor, S., Joshi, A., Scaria, V., Sivasubbu, S. (2016) Chamber Specific Gene Expression Landscape of the Zebrafish Heart. PLoS One. 11:e0147823
Shehata, B.M., Cundiff, C.A., Lee, K., Sabharwal, A., Lalwani, M.K., Davis, A.K., Agarwal, V., Sivasubbu, S., Iannucci, G.J., Gibson, G. (2015) Exome sequencing of patients with histiocytoid cardiomyopathy reveals a de novo NDUFB11 mutation that plays a role in the pathogenesis of histiocytoid cardiomyopathy. American journal of medical genetics. Part A. 167(9):2114-21
Dhiman, H., Kapoor, S., Sivadas, A., Sivasubbu, S., Scaria, V. (2015) zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs. PLoS One. 10:e0129997
Nambi, K.S., Abdul Majeed, S., Taju, G., Sivasubbu, S., Sundar Raj, N., Madan, N., Sahul Hameed, A.S. (2015) Development and Use of Retinal Pigmented Epithelial Cell Line from Zebrafish (Danio rerio) for Evaluating the Toxicity of Ultraviolet-B. Zebrafish. 12(1):21-32
Haque, S., Kaushik, K., Leonard, V.E., Kapoor, S., Sivadas, A., Joshi, A., Scaria, V., Sivasubbu, S. (2014) Short Stories on Zebrafish Long Noncoding RNAs. Zebrafish. 11(6):499-508
Singh, M., Bhartiya, D., Maini, J., Sharma, M., Singh, A.R., Kadarkaraisamy, S., Rana, R., Sabharwal, A., Nanda, S., Ramachandran, A., Mittal, A., Kapoor, S., Sehgal, P., Asad, Z., Kaushik, K., Vellarikkal, S.K., Jagga, D., Muthuswami, M., Chauhan, R.K., Leonard, E., Priyadarshini, R., Halimani, M., Malhotra, S., Patowary, A., Vishwakarma, H., Joshi, P., Bhardwaj, V., Bhaumik, A., Bhatt, B., Jha, A., Kumar, A., Budakoti, P., Lalwani, M.K., Meli, R., Jalali, S., Joshi, K., Pal, K., Dhiman, H., Laddha, S.V., Jadhav, V., Singh, N., Pandey, V., Sachidanandan, C., Ekker, S.C., Klee, E.W., Scaria, V., Sivasubbu, S. (2014) The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. Database : the journal of biological databases and curation. 2014:bau011
Agarwal, T., Lalwani, M.K., Kumar, S., Roy, S., Chakraborty, T.K., Sivasubbu, S., and Maiti, S. (2014) Morphological effects of g-quadruplex stabilization using a small molecule in zebrafish. Biochemistry. 53(7):1117-1124
Sivasubbu, S. (2014) Non-coding RNA based regulation of blood vessel development in zebrafish and relevance to humans. Molecular cytogenetics. 7:I10
Kaushik, K., Leonard, V.E., Kv, S., Lalwani, M.K., Jalali, S., Patowary, A., Joshi, A., Scaria, V., and Sivasubbu, S. (2013) Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish. PLoS One. 8(12):e83616
Sivasubbu, S., Sachidanandan, C., and Scaria, V. (2013) Time for the zebrafish ENCODE. Journal of genetics. 92(3):695-701
Soni, K., Choudhary, A., Patowary, A., Singh, A.R., Bhatia, S., Sivasubbu, S., Chandrasekaran, S., and Pillai, B. (2013) miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio. Nucleic acids research. 41(8):4470-80
Patowary, A., Purkanti, R., Singh, M., Chauhan, R., Singh, A.R., Swarnkar, M., Singh, N., Pandey, V., Torroja, C., Clark, M.D., Kocher, J.P., Clark, K.J., Stemple, D.L., Klee, E.W., Ekker, S.C., Scaria, V., and Sivasubbu, S. (2013) A sequence-based variation map of zebrafish. Zebrafish. 10(1):15-20
Jalali, S., Bhartiya, D., Lalwani, M.K., Sivasubbu, S., and Scaria, V. (2013) Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions. PLoS One. 8(2):e53823
Suryawanshi, H., Lalwani, M.K., Ramasamy, S., Rana, R., Scaria, V., Sivasubbu, S., and Maiti, S. (2012) Antagonism of microRNA Function in Zebrafish Embryos by Using Locked Nucleic Acid Enzymes (LNAzymes). Chembiochem : a European journal of chemical biology. 13(4):584-589
Ponnudurai, R.P., Basak, T., Ahmad, S., Bhardwaj, G., Chauhan, R.K., Singh, R.A., Lalwani, M.K., Sivasubbu, S., and Sengupta, S. (2012) Proteomic analysis of zebrafish (Danio rerio) embryos exposed to cyclosporine A. Journal of proteomics. 75(3):1004-17
Lalwani, M.K., Sharma, M., Singh, A.R., Chauhan, R.K., Patowary, A., Singh, N., Scaria, V., and Sivasubbu, S. (2012) Reverse Genetics Screen in Zebrafish Identifies a Role of miR-142a-3p in Vascular Development and Integrity. PLoS One. 7(12):e52588
Ding, Y., Sun, X., Huang, W., Hoage, T., Redfield, M., Kushwaha, S., Sivasubbu, S., Lin, X., Ekker, S., and Xu, X. (2011) Haploinsufficiency of Target of Rapamycin Attenuates Cardiomyopathies in Adult Zebrafish. Circulation research. 109(6):658-69
Clark, K.J., Balciunas, D., Pogoda, H.M., Ding, Y., Westcot, S.E., Bedell, V.M., Greenwood, T.M., Urban, M.D., Skuster, K.J., Petzold, A.M., Ni, J., Nielsen, A.L., Patowary, A., Scaria, V., Sivasubbu, S., Xu, X., Hammerschmidt, M., and Ekker, S.C. (2011) In vivo protein trapping produces a functional expression codex of the vertebrate proteome. Nature Methods. 8(6):506-512
Bhartiya, D., Maini, J., Sharma, M., Joshi, P., Laddha, S.V., Jalali, S., Patowary, A., Purkanti, R., Lalwani, M., Singh, A.R., Chauhan, R., Singh, N., Bhardwaj, A., Scaria, V., and Sivasubbu, S. (2010) FishMap Zv8 update--a genomic regulatory map of zebrafish. Zebrafish. 7(2):179-180
Petzold, A.M., Balciunas, D., Sivasubbu, S., Clark, K.J., Bedell, V.M., Westcot, S.E., Myers, S.R., Moulder, G.L., Thomas, M.J., and Ekker, S.C. (2009) Nicotine response genetics in the zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 106(44):18662-18667
Meli, R., Prasad, A., Patowary, A., Lalwani, M.K., Maini, J., Sharma, M., Singh, A.R., Kumar, G., Jadhav, V., Scaria, V., and Sivasubbu, S. (2008) FishMap: a community resource for zebrafish genomics. Zebrafish. 5(2):125-130
Sivasubbu, S., Balciunas, D., Amsterdam, A.,and Ekker, S.C. (2007) Insertional mutagenesis strategies in zebrafish. Genome biology. 8(1):S9
Pickart, M.A., Klee, E.W., Nielsen, A.L., Sivasubbu, S., Mendenhall, E.M., Bill B.R., Chen, E., Eckfeldt, C.E., Knowlton, M., Robu, M.E., Larson, J.D., Deng, Y., Schimmenti, L.A., Ellis, L.B., Verfaillie, C.M., Hammerschmidt, M., Farber, S.A., and Ekker, S.C. (2006) Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome. PLoS One. 1(1):e104
Balciunas, D., Wangensteen, K.J., Wilber, A., Bell, J., Geurts, A., Sivasubbu, S., Wang, X., Hackett, P.B., Largaespada, D.A., McIvor, R.S., and Ekker, S.C. (2006) Harnessing a High Cargo-Capacity Transposon for Genetic Applications in Vertebrates. PLoS Genetics. 2(11):e169
Sivasubbu, S., Balciunas, D., Davidson, A.E., Pickart, M.A., Hermanson, S.B., Wangensteen, K.J., Wolbrink, D.C., and Ekker, S.C. (2006) Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval development. Mechanisms of Development. 123(7):513-529
Pickart, M.A., Sivasubbu, S., Nielsen, A.L., Shriram, S., King, R.A., and Ekker, S.C. (2004) Functional genomics tools for the analysis of zebrafish pigment. Pigment cell research. 17(5):461-470
Balciunas, D., Davidson, A.E., Sivasubbu, S., Hermanson, S.B., Welle, Z., and Ekker, S.C. (2004) Enhancer trapping in zebrafish using the Sleeping Beauty transposon. BMC Genomics. 5(1):62
Hermanson, S., Davidson, A.E., Sivasubbu, S., Balciunas, D., and Ekker, S.C. (2004) Sleeping Beauty transposon for efficient gene delivery. The Zebrafish: Genetics, Genomics and Informatics, 2nd ed., Methods Cell Biol.. 77:349-362
Davidson, A.E., Balciunas, D., Mohn, D., Shaffer, J., Hermanson, S., Sivasubbu, S., Cliff, M.P., Hackett, P.B., and Ekker, S.C. (2003) Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon. Developmental Biology. 263(2):191-202