ZFIN Person: Sivasubbu, Sridhar

ZFIN ID: ZDB-PERS-060710-3

ZFIN ID: ZDB-PERS-060710-3

Sivasubbu, Sridhar

Email:	s.sivasubbu@igib.res.in
URL:	http://www.igib.res.in
Affiliation:	Sivasubbu Lab
Address:	Institute of Genomics and Integrative Biology (IGIB) Mall Road Delhi, 110 007 India
Country:	India
Phone:	+91-11-27662201
Fax:
ORCID ID:

BIOGRAPHY AND RESEARCH INTERESTS

PUBLICATIONS

Ichino, N., Serres, M.R., Urban, R.M., Urban, M.D., Treichel, A.J., Schaefbauer, K.J., Greif, L.E., Varshney, G.K., Skuster, K.J., McNulty, M.S., Daby, C.L., Wang, Y., Liao, H.K., El-Rass, S., Ding, Y., Liu, W., Anderson, J.L., Wishman, M.D., Sabharwal, A., Schimmenti, L.A., Sivasubbu, S., Balciunas, D., Hammerschmidt, M., Farber, S.A., Wen, X.Y., Xu, X., McGrail, M., Essner, J.J., Burgess, S.M., Clark, K.J., Ekker, S.C. (2020) Building the vertebrate codex using the gene breaking protein trap library. eLIFE. 9:

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

NON-ZEBRAFISH PUBLICATIONS