Complete List of Publications

(*indicates Corresponding Author)
2016

[67] Singh AR, Sivadas A, Sabharwal A, Vellarikal SK, Jayarajan R, Verma A, Kapoor S, Joshi A, Scaria V*, Sivasubbu S*
Chamber specific gene expression landscape of the zebrafish heart.
PLoS One. 2016 Jan 27;11(1):e0147823

[66] Vij S, Kuhl H, Kuznetsova I, Komissarov A, Yurchenko A, Heusden P, Singh S, Thevasagayam N, Sridatta P, Purushothaman K, Saju J, Jiang J, Mbandi S, Jonas M, Tong A, Mwangi S, Lau D, Ngoh S, Liew W, Shen X, Hon L, Drake J, Boitano M, Hall R, Chin C, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck F, Vurture G, Gopikrishna G, Kumar KV, Noble T, Scaria V, Sivasubbu S, Jerry D, O'Brien S, Schatz M, Dalmay T, Turner S, Lok S, Christoffels A, Orban L.
Long sequence reads followed by multi-layered scaffolding allow for a chromosome-level assembly of the Asian seabass genome.
PLoS Genetics (In Press)

[65] Ahirwar R, Vellarikkal SK, Sett A, Sivasubbu S, Scaria V, Bora U, Borthakur BB, Kataki AC, Sharma JD and Nahar P.
Aptamer-Assisted Detection of the Altered Expression of Estrogen Receptor Alpha in Human Breast Cancer
PLoS One 2016 (In Press)

2015

[64] Dhiman H, Kapoor S, Sivadas, A, Sivasubbu S*, Scaria V*
zflncRNApedia: a comprehensive online resource for zebrafish long non-coding RNAs
PLoS One. 2015 Jun 11;10(6):e0129997

[63] Aayush Gupta, Yugal Sharma, Kirti Deo, Shamsudheen Vellarikkal, Rijith Jayarajan, Vishal Dixit, Ankit Verma, Vinod Scaria*, Sridhar Sivasubbu*.
Case Report: Whole exome sequencing helps in accurate molecular diagnosis in siblings with a rare co-occurrence of paternally inherited 22q12 duplication and autosomal recessive non-syndromic ichthyosis.
F1000Res. 2015 Jul 31;4:446. doi: 10.12688/f1000research.6779.1. eCollection 2015.

[62] Vinod Scaria and Sridhar Sivasubbu.
Exome Sequence Analysis and Interpretation – Hand Book for Clinicians.
1st Ed. New Delhi. The Readers Paradise. 2015. (Book)

[61] Shehata BM, Cundiff CA, Lee K, Sabharwal A, Lalwani MK, Davis AK, Agrawal V, Sivasubbu S, Iannucci GJ, Gibson G.
Exome sequencing of patients with histiocytoid cardiomyopathy reveals a de novo NDUFB11 mutation that plays a role in the pathogenesis of histiocytoid cardiomyopathy.
Am J Med Genet A. 2015 Sep;167A(9):2114-21

[60] Vellarikkal SK, Dhiman H, Joshi K, Hasija Y, Sivasubbu S*, Scaria V*.
mit-o-matic: a comprehensive computational pipeline for clinical evaluation of mitochondrial variations from next-generation sequencing datasets.
Hum Mutat. 2015 Apr;36 (4):419-24

[59] Gupta A, Sharma YK, Vellarikkal SK, Jayarajan R, Dixit V, Verma A, Sivasubbu S*, Scaria V*.
Whole-exome sequencing solves diagnostic dilemma in a rare case of sporadic acrokeratosis verruciformis.
J Eur Acad Dermatol Venereol. 2015 Jan 26.

[58] Jalali S, Kohli S, Latka C, Bhatia S, Vellarikal SK, Sivasubbu S*, Scaria V*, Ramachandran R*
Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach
PLoS One. 2015 Jun 2;10(6):e0128711.

[57] Periwal V, Patowary A, Vellarikkal SK, Gupta A, Singh M, Mittal A, Jeyapaul S, Chauhan RK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K, Chauhan DS, Sivasubbu S*, Scaria V*.
Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome.
PLoS One. 2015 Apr 8;10(4):e0122979

[56] Behera BK, Das P, Maharana J, Paria P, Mandal SN, Meena DK, Sharma AP, Jayarajan R, Dixit V, Verma A, Vellarikkal SK, Scaria V, Sivasubbu S, Rao AR, Mohapatra T.
Draft Genome Sequence of the Extremely Halophilic Bacterium Halomonas salina Strain CIFRI1, Isolated from the East Coast of India.
Genome Announc. 2015 Jan 8;3(1). pii: e01321-14.

[55] Nambi KS, Majeed SA, Taju G, Sivasubbu S, Raj NS, Madan N, Hameed AS.
Development and use of retinal pigmented epithelial cell line from zebrafish (Danio rerio) for evaluating the toxicity of ultraviolet-B.
Zebrafish. 2015 Feb;12(1):21-32.

2014
[54] Haque S, Kaushik K, Elvin V, Kapoor S, Sivadas A, Joshi A, Scaria V*, Sivasubbu S*
Short stories on zebrafish long noncoding RNAs
Zebrafish. 2014 Dec;11(6):499-508.

[53] Vellarikkal SK, Patowary A, Singh M, Kumari R, Faruq M, Master DC, Sivasubbu S* & Scaria V*
Exome sequencing reveals a novel mutation p.L325H in KRT5 gene associated with autosomal dominant Epidermolysis Bullosa Simplex in a large family from Western India
Human Genome Variation. 2014,1, Article number: 14007

[52] Rajpathak SN, Vellarikkal SK,Patowary A, Scaria V*, Sivasubbu S* & Deobagkar DD*
Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome.
PLoS One. 2014 Jun 16;9(6):e100076

[51] Shubha Vij, Kathiresan Purushothaman, G.Gopikrishna, Doreen Lau, Jolly M.Saju, K. V.Shamsudheen, K.Vinaya Kumar, V.S.Basheer, A.Gopalakrishnan, Mohammad S.Hossain, Sridhar Sivasubbu, Vinod Scaria, J.K. Jena, A.G.Ponniah and László Orbán
Barcoding of Asian seabass across its geographic range provides evidence for its bifurcation into two distinct species.
Front. Mar. Sci., 05 August 2014

[50] Singh M, Bhartiya D, Maini J, Sharma M, Singh AR, Kadarkaraisamy S, Rana R, Sabharwal A, Nanda S, Ramachandran A, Mittal A, Kapoor S, Sehgal P, Asad Z, Kaushik K, Vellarikkal SK, Jagga D, Muthuswami M, Chauhan RK, 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 MK, Meli R, Jalali S, Joshi K, Pal K, Dhiman H, Laddha SV, Jadhav V, Singh N, Pandey V, Sachidanandan C, Ekker SC, Klee EW, Scaria V*, Sivasubbu S*.
The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation.
Database (Oxford). 2014 Feb 26;2014(0):bau011.

[49] Tiwari PK, Joshi K, Rehman R, Bhardwaj V, Shamsudheen KV, Sivasubbu S*, Scaria V*.
Draft Genome Sequence of Urease-Producing Sporosarcina pasteurii with Potential Application in Biocement Production.
Genome Announc. 2014 Jan 30;2(1). pii: e01256-13.

[48] Agarwal T, Lalwani MK, Kumar S, Roy S, Chakraborty TK, Sivasubbu S*, Maiti S*.
Morphological effects of g-quadruplex stabilization using a small molecule in zebrafish. Biochemistry. 2014 Feb 25;53(7):1117-24.


2013

[47] Kaushik K, Leonard VE, Kv S, Lalwani MK, Jalali S, Patowary A, Joshi A, ScariaV*, Sivasubbu S*.
Dynamic expression of long non-coding RNAs (lncRNAs) in adult zebrafish.
PLoS One. 2013 Dec 31;8(12):e83616.

[46] Sivasubbu S*, Sachidanandan C*, Scaria V*.
Time for the zebrafish ENCODE.
J Genet. 2013 Dec;92(3):695-701.

[45] Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S*, Scaria V*.
Draft Genome Sequence of a Multidrug-Resistant Clinical Isolate of Mycobacterium tuberculosis Belonging to a Novel Spoligotype.
Genome Announc. 2013 Nov 21;1(6). pii:e00965-13.

[44] Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS*, Sivasubbu S, Scaria V*.
Draft Genome Sequence of Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate OSDD515, Belonging to the Uganda I Genotype.
Genome Announc. 2013 Nov 21;1(6). pii: e00750-13.

[43] Karuthedath Vellarikkal S, Vir Singh A, Kumar Singh P, Garg P, Mohan Katoch V, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V*, Sivasubbu S*.
Draft Genome Sequence of an Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate of the Ural Strain OSDD493.
Genome Announc. 2013 Nov 7;1(6). pii: e00928-13.

[42] Salleh MZ*, Teh LK, Lee LS, Ismet RI, Patowary A, Joshi K, Pasha A, Ahmed AZ, Janor RM, Hamzah AS, Adam A, Yusoff K, Hoh BP, Hatta FH, Ismail MI, Scaria V*, Sivasubbu S*.
Systematic pharmacogenomics analysis of a Malay whole genome: proof of concept for personalized medicine.
PLoS One. 2013 Aug 23;8(8):e71554.

[41] Karuthedath Vellarikkal S, Patowary A, Singh M, Periwal V, Singh AV, Singh PK, Garg P, Mohan Katoch V, Katoch K, Jangir PK, Sharma R; Open Source Drug Discovery Consortium, Chauhan DS, Scaria V*, Sivasubbu S*.
Draft Genome Sequence of a Clinical Isolate of Multidrug-Resistant Mycobacterium tuberculosis East African Indian Strain OSDD271.
Genome Announc. 2013 Aug 1;1(4). pii: e00541-13.

[40] Bhartiya D, Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B, Jain S, Sati S,Sengupta S, Sachidanandan C, Raghava GP, Sivasubbu S, Scaria V.
lncRNome: a comprehensive knowledgebase of human long noncoding RNAs.
Database (Oxford). 2013 Jul 11;2013:bat034.

[39] Patowary A, Purkanti R, Singh M, Chauhan R, Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher JP, Clark KJ, Stemple DL, Klee EW, Ekker SC*, Scaria V*, Sivasubbu S*.
A sequence-based variation map of zebrafish.
Zebrafish. 2013 Mar;10(1):15-20.

[38] Soni K, Choudhary A, Patowary A, Singh AR, Bhatia S, Sivasubbu S, Chandrasekaran S, Pillai B.
miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio.
Nucleic Acids Res. 2013 Apr;41(8):4470-80.

[37] Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S*, Scaria V*.
Systematic transcriptome wide analysis of lncRNA-miRNA interactions.
PLoS One. 2013;8(2):e53823.

2012
[36] Lalwani MK, Sharma M, Singh AR, Chauhan RK, Patowary A, Singh N, Scaria V*, Sivasubbu S*.
Reverse genetic screen in zebrafish identify role of miR-142a-3p in vascular development and integrity.
PLoS One. 2012;7(12):e52588

[35] Bargaje R, Alam MP, Patowary A, Sarkar M, Ali T, Gupta S, Garg M, Singh M, Purkanti R, Scaria V, Sivasubbu S, Brahmachari V, Pillai B.
Proximity of H2A.Z containing nucleosome to the transcription start site influences gene expression levels in the mammalian liver and brain.
Nucleic Acids Res. 2012 Oct 1;40(18):8965-78.

[34] Bhartiya D, Kapoor S, Jalali S, Sati S, Kaushik K, Sachidanandan C, Sivasubbu S, Scaria V.
Conceptual approaches for lncRNA drug discovery and future strategies.
Expert Opin Drug Discov. 2012 Jun;7(6):503-13

[33] Patowary A, Purkanti R, Singh M, Chauhan RK, Bhartiya D, Dwivedi OP, Chauhan G, Bharadwaj D, Sivasubbu S*, Scaria V*.
Systematic analysis and functional annotation of variations in the genome of an Indian individual.
Hum Mutat. 2012 Jul;33(7):1133-40.

[32] Ahluwalia JK, Soni K, Sivasubbu S, Brahmachari V.
Modeling SNP mediated differential targeting of homologous 3'UTR by microRNA.
RNA Biol. 2012 Mar;9(3):351-60

[31] Suryawanshi H, Lalwani MK, Ramasamy S, Rana R, Scaria V, Sivasubbu S*, Maiti S*.
Antagonism of microRNA function in zebrafish embryos by using locked nucleic acid enzymes (LNAzymes).
Chembiochem. 2012 Mar 5;13(4):584-9.

[30] Sati S, Tanwar VS, Kumar KA, Patowary A, Jain V, Ghosh S, Ahmad S, Singh M, Reddy SU, Chandak GR, Raghunath M, Sivasubbu S, Chakraborty K, Scaria V, Sengupta S.
High resolution methylome map of rat indicates role of intragenic DNA methylation in identification of coding region.
PLoS One. 2012;7(2):e31621

[29] Gireesh-Babu P, Nilambari Pawar, Krishnan P, Pavan Kumar A, Zaidi SGS, Bhartiya D, Kumar N, Sivasubbu S, Rajendran KV and Chaudhari A.
Functional characterization of the zebrafish gadd45α b gene promoter and its application as a biosensor.
Current Science. 2012. Vol. 103, No. 4: 388-394.

[28] Kandoi G, Nanda A, Scaria V*, Sivasubbu S*.
A case for pharmacogenomics in management of cardiac arrhythmias.
Indian Pacing Electrophysiol J. 2012 Mar;12(2):54-64.

[27] Patowary A, Chauhan RK, Singh M, Kv S, Periwal V, Kp K, Sapkal GN, Bondre VP, Gore MM, Sivasubbu S*, Scaria V*.
De novo identification of viral pathogens from cell culture hologenomes.
BMC Res Notes. 2012 Jan 6;5:11.

[26] Ponnudurai RP, Basak T, Ahmad S, Bhardwaj G, Chauhan RK, Singh RA, Lalwani MK, Sivasubbu S*, Sengupta S*.
Proteomic analysis of zebrafish (Danio rerio) embryos exposed to cyclosporine A.
J Proteomics. 2012 Jan 4;75(3):1004-17

2011
[25] Clark KJ, Balciunas D, Pogoda HM, Ding Y, Westcot SE, Bedell VM, Greenwood TM, Urban MD, Skuster KJ, Petzold AM, Ni J, Nielsen AL, Patowary A, Scaria V, Sivasubbu S, Xu X, Hammerschmidt M, Ekker SC.
In vivo protein trapping produces a functional expression codex of the vertebrate proteome.
Nature Methods. 2011. Vol.8 No.6.506-512 [Featured Article]

[24] Dissanayake VHW, Samarakoon P, Scaria V, Patowary A, Sivasubbu S, Gokhale, RS.
The Sri Lankan Personal Genome Project: an overview.
Sri Lanka Journal of Biomedical Informatics. 2011. 2(1): 4-8.

[23] Ding Y, Sun X, Huang W, Hoage T, Redfield M, Kushwaha S, Sivasubbu S, Lin X, Ekker S and Xu X.
Haploinsufficiency of Target of Rapamycin Attenuates Cardiomyopathies in Adult Zebrafish.
Circulation Research. 2011 Sep 2;109(6):658-69.

2010
[22] Bhartiya D, Maini J, Sharma M, Joshi P, Laddha S, Jalali S, Patowary A, Purkanti R, Lalwani M, Singh R, Chauhan R, Singh N, Bhardwaj A, Scaria V, Sivasubbu S*.
FishMap Zv8 update – A Genomic Regulatory Map of Zebrafish.
Zebrafish. 2010. 7(2): 179-180

2009
[21] Petzold AM, Balciunas D, Sivasubbu S, Clark KJ, Bedell VM, Westcot SE, Myers SR, Moulder GL, Thomas MJ, Ekker SC.
Nicotine response genetics in the zebrafish.
Proc Natl Acad Sci U S A 2009. Nov 3;106(44):18662-7.

2008
[20] 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*.
FishMap: A community resource for zebrafish genomics.
Zebrafish. 2008. 5(2):125-30. [Cover Article]

[19] Kumar, N., Patowary, A., Sivasubbu, S., Petersen, M., Maiti, S.
Silencing c-MYC Expression by Targeting Quadruplex in P1 Promoter Using Locked Nucleic Acid Trap.
Biochemistry, 2008; 47; 13179–13188

[18] Indian Genome Variation Consortium (as co-author of the consortia).
Genetic Landscape of the People of India: a Canvas for Disease Gene Exploration.
J Genetics 2008. 87 P 3-20. Cover Article

2007
[17] Sivasubbu, S., Balciunas, D., Amsterdam, A and Ekker, S.C.
Insertional mutagenesis strategies in zebrafish.
Genome Biology. 2007. 8(Suppl I):S9

2006
[16] Sivasubbu, S., Balciunas, D., Davidson, A. E., Pickart, M. A., Hermanson, S.B., Wangesteen, K., Wolbrink, D and Ekker, S.C.
Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval developmental.
Mechanism of Development. 2006. 123(7): 513-529

[15] 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. M., Verfaillie, C. M., Hammerschmidt, M., Farber, S. A., and Ekker, S. C.
Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome.
PLoS ONE 2006. 1(1): e104.

[14] Balciunas, D., Wangensteen, K, J., Wilber, A., Bell, J., Geurts, A., Sivasubbu, S., Wnag, X., Hackett, P. B., Largaespada, D., McIvor, R. S. and Ekker, S. C.
Harnessing a high cargo-capacity transposon for genetic applications in vertebrates.
PLoS Genetics 2006. 2(11):e169.

2004
[13] Pickart, M.A., Sivasubbu, S., Neilsen, A.L., Shriram, S., King, R.A and Ekker, S.C.
Functional genomics tools for the analysis of zebrafish pigment.
Pigment Cell Research. 2004. 17:461-470.

[12] Balciunas, D., Davidson, A. E., Sivasubbu, S., Hermanson, S.B., Welle, Z and Ekker, S.C.
Enhancer trapping in zebrafish using the Sleeping Beauty transposon.
BMC Genomics. 2004. 5:62.

[11] Hermanson, S., Davidson., A.E., Sivasubbu, S., Balciunas,D and Ekker, S.C.
Sleeping Beauty transposon for efficient gene delivery.
Methods in Cell Biology. The Zebrafish: Genetics, Genomics and Informatics. 2004. 77:351-364

[10] Haniffa, M. A., Sridhar, S & Nagarajan, M. .
Induction of triploidy and tetraploidy in stinging catfish, Heteropneustes fossilis (Bloch), using heat shock.
Aquaculture Research. 2004. 35(10): 937-942.

[09] Haniffa, M. A., Sridhar, S and Nagarajan, M.
Hormonal manipulation of sex in stinging catfish Heteropneustes fossilis (Bloch).
Current Science. 2004. 86(7): 1012-1017.

2002 -2003
[08] Davidson, A. E., Balciunas, D., Mohn, D., Shaffer, J., Hermanson, S., Sivasubbu, S., Cliff, M.P., Hackett, P.B and Ekker, S.C.
Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon.
Developmental Biology. 2003. 263:191-202.

[07] Haniffa,M.A., Jesu Arockia Raj, A., Sethuramalingam, T.A and Sridhar, S.
Digestibility of lipid in different feeds by stripped murrel Channa Striatus.
J. Aqua. Trop. 2002. 17(3):185-191.

[06] Haniffa, M.A and Sridhar, S.
Induced spawning of spotted murrel (Channa punctatus) and catfish (Heteropneustus fossilis) using human chorionic gonodotropin and synthetic hormone (Ovaprim).
Veterinarski Arhiv. 2002. 72(1):51-56.

2000 and prior
[05] Haniffa, M.A., Jesu Arockia Raj, A and Sridhar, S.
Weaning diet for striped murrel Channa Straitus.
Fisheries Technology. 1999. 36 (2):116-119.

[04] Arunachalam, M., Johnson, J.A., Manimekalan, A and Sridhar, S.
New Record of Heteropneustes microps (Gunther) (CLARIIDAE: Heteropneusitidae) from Western Ghats Rivers. INDIA.
J. Bom. Nat. His. Society. 1999. 96 (2):330-332.

[03] Sridhar, S and Haniffa, M.A.
Interspecific hybridization between the catfishes Heteropneustes fossilis (Bloch) and Heteropneustes microps (Gunther) (Siluridae: Heteropneustidae).
Current Science. 1999. 76:871-873.

[02] Sridhar, S., Vijayakumar, C and Haniffa, M.A.
First report on induced spawning and establishment of a captive population for a fish, Ompok bimaculatus in India.
Current Science. 1998. 75:1066-1068.

[01] Vijayakumar, C., Sridhar, S. and Haniffa, M.A.
Low cost breeding and hatching techniques of the catfish Heteropneustes fossilis for small scale fish farmers.
NAGA. 1998. 21 No.4:15-17.