Sridhar Sivasubbu, PhD - Publication & Tech

Technology Commercialization

2021 - IMDX SARS-CoV2 Multiplex RT-PCR Assays. Two Assays Licensed to Siemens Healthcare Private Limited.

2020 - COVIDsure Multiplex Realtime RT-PCR kit. Licensed to Trivitron Healthcare Pvt Ltd, India.

2018 - Molecular diagnostic assays for 27 genetic diseases. Licensed to Dr Lal Path Lab Ltd, India.

2016 - Next Generation Sequencing based approach for diagnosis of Mitochondrial Disorders. Licensed to Eurofins Clinical Genetics India Ltd and marketed in the brand name MitoSure.

Scientific Publications

Articles Published - 163

Complete list of publication is available at: http://tiny.cc/yfu5vz

(*Corresponding author)

2024

[163] Senthivel V, Jolly B, Vr A, Bajaj A, Bhoyar R, Imran M, Vignesh H, Divakar MK, Sharma G, Rai N, Kumar K, Mp J, Krishna M, Shenthar J, Ali M, Abqari S, Nadri G, Scaria V, Naik N*, Sivasubbu S*.

Whole genome sequencing of families diagnosed with cardiac channelopathies reveals structural variants missed by whole exome sequencing.

J Hum Genet. 2024 Jun 18. doi: 10.1038/s10038-024-01265-2.

[162] Sabharwal A, Gupta V, Kv S, Kumar Manokaran R, Verma A, Mishra A, Bhoyar RC, Jain A, Sivadas A, Rawat S, Jolly B, Mohanty S, Gulati S, Gupta N, Kabra M*, Scaria V*, Sivasubbu S*.

Whole genome sequencing followed by functional analysis of genomic deletion encompassing ERCC8 and NDUFAF2 genes in a non-consanguineous Indian family reveals dysfunctional mitochondrial bioenergetics leading to infant mortality.

Mitochondrion. 2024 Mar;75:101844. doi: 10.1016/j.mito.2024.101844.

[161] Gupta V, Jolly B, Bhoyar RC, Divakar MK, Jain A, Mishra A, Senthivel V, Imran M, Scaria V*, Sivasubbu S*.

Spectrum of rare and common mitochondrial DNA variations from 1029 whole genomes of self-declared healthy individuals from India.

Comput Biol Chem. 2024 Jun 10;112:108118. doi: 10.1016/j.compbiolchem.2024.108118.

[160] Angom RS, Joshi A, Patowary A, Sivadas A, Ramasamy S, K V S, Kaushik K, Sabharwal A, Lalwani MK, K S, Singh N, Scaria V, Sivasubbu S.

Forward genetic screen using a gene-breaking trap approach identifies a novel role of grin2bb-associated RNA transcript (grin2bbART) in zebrafish heart function.

Front Cell Dev Biol. 2024 Mar 8;12:1339292. doi: 10.3389/fcell.2024.1339292.

[159] Sivadas A, Sahana S, Jolly B, Bhoyar RC, Jain A, Sharma D, Imran M, Senthivel V, Divakar MK, Mishra A, Mukhopadhyay A, Gibson G, Narayan KV, Sivasubbu S, Scaria V, Kurpad AV.

Landscape of pharmacogenetic variants associated with non-insulin antidiabetic drugs in the Indian population.

BMJ Open Diabetes Res Care. 2024 Mar 12;12(2):e003769. doi: 10.1136/bmjdrc-2023-003769.

[158] Sivadas A, Rathore S, Sahana S, Jolly B, Bhoyar RC, Jain A, Sharma D, Imran M, Senthilvel V, Divakar MK, Mishra A, Sivasubbu S, Scaria V.

The genomic landscape of CYP2D6 variation in the Indian population.

Pharmacogenomics. 2024 Feb;25(3):147-160. doi: 10.2217/pgs-2023-0233.

[157] Verma D, Kapoor S, Kumari S, Sharma D, Singh J, Benjamin M, Bakhshi S, Seth R, Nayak B, Sharma A, Pramanik R, Palanichamy JK, Sivasubbu S, Scaria V, Arora M, Kumar R, Chopra A.

Decoding the genetic symphony: Profiling protein-coding and long noncoding RNA expression in T-acute lymphoblastic leukemia for clinical insights.

PNAS Nexus. 2024 Jan 12;3(2):pgae011. doi: 10.1093/pnasnexus/pgae011.

[156] Tyagi N, Uppili B, Sharma P, Parveen S, Saifi S, Jain A, Sonakar A, Ahmed I, Sahni S, Shamim U, Anand A, Suroliya V, Asokachandran V, Srivastava A, Sivasubbu S, Scaria V, Faruq M.

Investigation of RFC1 tandem nucleotide repeat locus in diverse neurodegenerative outcomes in an Indian cohort.

Neurogenetics. 2024 Jan;25(1):13-25. doi: 10.1007/s10048-023-00736-6

2023

[155] Gupta P, Arvinden VR, Thakur P, Bhoyar RC, Saravanakumar V, Gottumukkala NV, Goswami SG, Nafiz M, Iyer AR, Vignesh H, Soni R, Bhargava N, Gunda P, Jain S, Gupta V, Sivasubbu S, Scaria V, Ramalingam S.

Scalable noninvasive amplicon-based precision sequencing (SNAPseq) for genetic diagnosis and screening of β-thalassemia and sickle cell disease using a next-generation sequencing platform. Front Mol Biosci. 2023 Dec 13;10:1244244. doi: 10.3389/fmolb.2023.1244244.

[154] Rophina M, Kek TL, Sivasubbu S, Scaria V, Salleh MZ.

In silico genotyping of blood group alleles using WGS data: a comparative study of the Orang Asli in Peninsular Malaysia.

J Genet. 2023;102:42.

[153] Singh P, Kaur L, Ghose S, Varshney S, Jyothi V, Ghosh S, Kommineni P, Kv S, Scaria V, Sivasubbu S, Chandak GR, Sengupta S.

Maternal-Periconceptional Vitamin B12 Deficiency in Wistar Rats Leads to Sex-Specific Programming for Cardiometabolic Disease Risk in the Next Generation.

J Nutr. 2023 Dec;153(12):3382-3396. doi: 10.1016/j.tjnut.2023.08.032.

[152] Rophina M, Bhoyar RC, Imran M, Senthivel V, Divakar MK, Mishra A, Vatsyayan A, Jolly B, Sivasubbu S, Scaria V.

Genetic landscape of human platelet antigen variants in the Indian population analysed from 1029 whole genomes.

Int J Immunogenet. 2023 Jun;50(3):134-143. doi: 10.1111/iji.12622.

[151] Roy SS, Sharma S, Rizvi ZA, Sinha D, Gupta D, Rophina M, Sehgal P, Sadhu S, Tripathy MR, Samal S, Maiti S, Scaria V, Sivasubbu S, Awasthi A, Harshan KH, Jain S, Chowdhury S.

G4-binding drugs, chlorpromazine and prochlorperazine, repurposed against COVID-19 infection in hamsters.

Front Mol Biosci. 2023 Mar 16;10:1133123. doi: 10.3389/fmolb.2023.1133123.

[150] Divakar MK, Jain A, Bhoyar RC, Senthivel V, Jolly B, Imran M, Sharma D, Bajaj A, Gupta V, Scaria V*, Sivasubbu S*.

Whole-genome sequencing of 1029 Indian individuals reveals unique and rare structural variants. J Hum Genet. 2023 Feb 22. doi: 10.1038/s10038-023-01131-7.

[149] Rophina M, Bhoyar RC, Imran M, Senthivel V, Divakar MK, Mishra A, Jolly B, Sivasubbu S, Scaria V.

Genetic landscape of human neutrophil antigen variants in India from population-scale genomes. HLA. 2023 Mar;101(3):262-269. doi: 10.1111/tan.14938.

[148] Bhatt L, Bhoyar RC, Jolly B, Israni R, Vignesh H, Scaria V*, Sivasubbu S*.

The genome sequence of lumpy skin disease virus from an outbreak in India suggests a distinct lineage of the virus. Arch Virol 2023 Feb5;168(3):81.doi:10.1007/s00705-023-05705-w.

2022

[147] Bajaj A, Senthivel V, Bhoyar R, Jain A, Imran M, Rophina M, Divakar MK, Jolly B, Verma A, Mishra A, Sharma D, Deepti S, Sharma G, Bansal R, Yadav R, Scaria V, Naik N, Sivasubbu S*.

1029 genomes of self-declared healthy individuals from India reveal prevalent and clinically relevant cardiac ion channelopathy variants.

Hum Genomics. 2022 Aug 5;16(1):30. doi: 10.1186/s40246-022-00402-2.

[146] Prakrithi P, Jha P, Jaiswal J, Sharma D, Bhoyar RC, Jain A, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M.

Landscape of Variability in Chemosensory Genes Associated With Dietary Preferences in Indian Population: Analysis of 1029 Indian Genomes.

Front Genet. 2022 Jul 12;13:878134. doi: 10.3389/fgene.2022.878134.

[145] Panda G, Mishra N, Sharma D, Kutum R, Bhoyar RC, Jain A, Imran M, Senthilvel V, Divakar MK, Mishra A, Garg P, Banerjee P, Sivasubbu S, Scaria V, Ray A.

Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum.

Front Pharmacol. 2022 Jul 5;13:858345. doi: 10.3389/fphar.2022.858345.

[144] Kemp SA, Cheng MTK, Hamilton WL, Kamelian K; Indian SARS-CoV-2 Genomics Consortium (INSACOG), Singh S, Rakshit P, Agrawal A, Illingworth CJR, Gupta RK.

Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers.

Sci Rep. 2022 Jun 21;12(1):10492. doi: 10.1038/s41598-022-14411-7.

[143] Mathew S, Sivasubbu S*.

Long Non Coding RNA Based Regulation of Cerebrovascular Endothelium.

Front Genet. 2022 Apr 13;13:834367. doi: 10.3389/fgene.2022.834367.

[142] Vanlallawma A, Lallawmzuali D, Pautu JL, Scaria V, Sivasubbu S, Kumar NS.

Whole exome sequencing of pediatric leukemia reveals a novel InDel within FLT-3 gene in AML patient from Mizo tribal population, Northeast India.

BMC Genom Data. 2022 Mar 28;23(1):23. doi: 10.1186/s12863-022-01037-x.

[141] Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, A K V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B M P, Rajagopal RE, Ramya J E, Devi P N, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, Meyakumla, S S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, B K B, Scaria V, Sivasubbu S*.

Genetic epidemiology of autoinflammatory disease variants in Indian population from 1029 whole genomes.

J Genet Eng Biotechnol. 2021 Dec 14;19(1):183. doi: 10.1186/s43141-021-00268-2.

[140] Sahana S, Bhoyar RC, Sivadas A, Jain A, Imran M, Rophina M, Senthivel V, Kumar Diwakar M, Sharma D, Mishra A, Sivasubbu S, Scaria V.

Pharmacogenomic landscape of Indian population using whole genomes.

Clin Transl Sci. 2022 Apr;15(4):866-877. doi: 10.1111/cts.13153. Epub 2022 Mar 26.

[139] Prakrithi P, Singhal K, Sharma D, Jain A, Bhoyar RC, Imran M, Senthilvel V, Divakar MK, Mishra A, Scaria V, Sivasubbu S, Mukerji M.

An Alu insertion map of the Indian population: identification and analysis in 1021 genomes of the IndiGen project.

NAR Genom Bioinform. 2022 Feb 15;4(1):lqac009. doi: 10.1093/nargab/lqac009.

[138] Madathil Govindaraj G, Jain A, Edavazhippurath A, Bhoyar RC, Dhanasooraj D, Mishra A, Gupta V, Nair M, Shiny PM, Uppuluri R, Kumar A, Kashyap A, Ajith Kumar VT, Shankaran G, Senthivel V, Imran M, Kumar Divakar M, Sawant S, Dalvi A, Madkaikar M, Raj R, Sivasubbu S, Scaria V.

Clinical, immunological and genomic characteristics of children with X-linked agammaglobulinemia from Kerala, South India.

Hum Immunol. 2022 Apr;83(4):335-345. doi: 10.1016/j.humimm.2022.01.003.

[137] Gupta A, Bhoyar R, Mirza S, Jolly B, Senthivel V, Shamnath A, Divakar MK, Imran M, Gupta V, Agrawal SJ, Mukhida S, Sivasubbu S, Scaria V.

SARS-CoV-2 vaccine breakthrough infection following a previous infection in a healthcare worker.

J Infect. 2022 Mar;84(3):418-467. doi: 10.1016/j.jinf.2021.10.008.

[136] Singh UB, Rophina M, Chaudhry R, Senthivel V, Bala K, Bhoyar RC, Jolly B, Jamshed N, Imran M, Gupta R, Aggarwal P, Divakar MK, Sinha S, Arvinden VR, Bajaj A, Shamnath A, Jain A; COVID CBNAAT CORE GROUP, Scaria V, Sivasubbu S, Guleria R.

Variants of concern responsible for SARS-CoV-2 vaccine breakthrough infections from India.

J Med Virol. 2022 Apr;94(4):1696-1700. doi: 10.1002/jmv.27461.

[135] Thiruvengadam R, Awasthi A, Medigeshi G, Bhattacharya S, Mani S, Sivasubbu S,..... Agrawal A, Vrati S, Bhatnagar S, Garg PK; Department of Biotechnology India Consortium for COVID-19 research.

Effectiveness of ChAdOx1 nCoV-19 vaccine against SARS-CoV-2 infection during the delta (B.1.617.2) variant surge in India: a test-negative, case-control study and a mechanistic study of post-vaccination immune responses.

Lancet Infect Dis. 2022 Apr;22(4):473-482. doi: 10.1016/S1473-3099(21)00680-0.

[134] Sharma B, Subramaniam YJ, Ayyappa Raja D, Aggarwal A, Sivasubbu S, Natarajan VT.

Reverse Genetic Approach to Identify Regulators of Pigmentation using Zebrafish.

J Vis Exp. 2022 Mar 1;(181). doi: 10.3791/62955.

[133] Vanlallawma A, Lallawmzuali D, Pautu JL, Scaria V, Sivasubbu S, Kumar NS.

Whole exome sequencing of pediatric leukemia reveals a novel InDel within FLT-3 gene in AML patient from Mizo tribal population, Northeast India.

BMC Genom Data. 2022 Mar 28;23(1):23. doi: 10.1186/s12863-022-01037-x.

2021

[132] Sehgal P, Mathew S, Sivadas A, Ray A, Tanwar J, Vishwakarma S, Ranjan G, Shamsudheen KV, Bhoyar RC, Pateria A, Leonard E, Lalwani M, Vats A, Pappuru RR, Tyagi M, Jakati S, Sengupta S, B K B, Chakrabarti S, Kaur I, Motiani RK, Scaria V*, Sivasubbu S*.

LncRNA VEAL2 regulates PRKCB2 to modulate endothelial permeability in diabetic retinopathy.

EMBO J. 2021 Jun 28:e107134. doi: 10.15252/embj.2020107134.

[131] Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, A K V, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, B M P, Rajagopal RE, J ER, P ND, Bajaj A, Gupta V, Mathew S, Goswami S, Mangla M, Prakash S, Joshi K, S S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, Binukumar B K, Scaria V*, Sivasubbu S*.

IndiGenomes: a comprehensive resource of genetic variants from over 1000 Indian genomes.

Nucleic Acids Res. 2021 Jan 8;49(D1):D1225-D1232. doi: 10.1093/nar/gkaa923.

[130] Mlcochova P, Kemp S, Dhar MS, Papa G, Meng B, Ferreira IATM,....Agrawal A, Gupta RK.

SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion.

Nature. 2021 Sep 6. doi: 10.1038/s41586-021-03944-y.

(INSACOG Consortia co-author)

[129] Dhar MS, Marwal R, Vs R, Ponnusamy K, Jolly B, Bhoyar RC, Sardana V,.....Indian SARS-CoV-2 Genomics Consortium (INSACOG).

Genomic characterization and epidemiology of an emerging SARS-CoV-2 variant in Delhi, India.

Science. 2021 Nov 19;374(6570):995-999. doi: 10.1126/science.abj9932.

(INSACOG Consortia co-author)

[128] Bhoyar RC, Senthivel V, Jolly B, Imran M, Jain A, Divakar MK, Scaria V, Sivasubbu S*.

An optimized, amplicon-based approach for sequencing of SARS-CoV-2 from patient samples using COVIDSeq assay on Illumina MiSeq sequencing platforms.

STAR Protoc. 2021 Sep 17;2(3):100755. doi: 10.1016/j.xpro.2021.100755.

[127] Mahadevan R, Bhoyar RC, Viswanathan N, Rajagopal RE, Essaki B, Suroliya V, Chelladurai R, Sankaralingam S, Shanmugam G, Vayanakkan S, Shamim U, Mathur A, Jain A, Imran M, Faruq M, Scaria V*, Sivasubbu S*, Kalyanaraman S*.

Genomic analysis of patients in a South Indian community with autosomal dominant cortical tremor, myoclonus and epilepsy (ADCME) suggests a founder repeat expansion mutation in the SAMD12 gene.

Brain Communications. 2021, fcaa214, https://doi.org/10.1093/braincomms/fcaa214

[126] Jain A, Govindaraj GM, Edavazhippurath A, Faisal N, Bhoyar RC, Gupta V, Uppuluri R, Manakkad SP, Kashyap A, Kumar A, Divakar MK, Imran M, Sawant S, Dalvi A, Chakyar K, Madkaikar M, Raj R, Sivasubbu S, Scaria V.

Whole genome sequencing identifies novel structural variant in a large Indian family affected with X-linked agammaglobulinemia.

PLoS One. 2021 Jul 12;16(7):e0254407. doi: 10.1371/journal.pone.0254407.

[125] Sharma D, Sehgal P, Sivasubbu S, Scaria V.

A genome-wide circular RNA transcriptome in rat.

Biol Methods Protoc. 2021 Sep 7;6(1):bpab016. doi: 10.1093/biomethods/bpab016.

[124] Sahana S, Sivadas A, Mangla M, Jain A, Bhoyar RC, Pandhare K, Mishra A, Sharma D, Imran M, Senthivel V, Divakar MK, Rophina M, Jolly B, Batra A, Sharma S, Siwach S, Jadhao AG, Palande NV, Jha GN, Ashrafi N, Mishra PK, Vidhya AK, Jain S, Dash D, Kumar NS, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S, Mahadevan R, Kandasamy S, Devi P, Rajagopal RE, Ramya JE, Devi PN, Bajaj A, Gupta V, Mathew S, Goswami S, Prakash S, Joshi K, Kumla M, Sreedevi S, Gajjar D, Soraisham R, Yadav R, Devi YS, Gupta A, Mukerji M, Ramalingam S, Binukumar BK, Sivasubbu S, Scaria V.

Pharmacogenomic landscape of COVID-19 therapies from Indian population genomes.

Pharmacogenomics. 2021 Jul;22(10):603-618. doi: 10.2217/pgs-2021-0028.

[123] Bhoyar RC, Jain A, Sehgal P, Divakar MK, Sharma D, Imran M, Jolly B, Ranjan G, Rophina M, Sharma S, Siwach S, Pandhare K, Sahoo S, Sahoo M, Nayak A, Mohanty JN, Das J, Bhandari S, Mathur SK, Kumar A, Sahlot R, Rojarani P, Lakshmi JV, Surekha A, Sekhar PC, Mahajan S, Masih S, Singh P, Kumar V, Jose B, Mahajan V, Gupta V, Gupta R, Arumugam P, Singh A, Nandy A, P V R, Jha RM, Kumari A, Gandotra S, Rao V, Faruq M, Kumar S, Reshma G B, Varma G N, Roy SS, Sengupta A, Chattopadhyay S, Singhal K, Pradhan S, Jha D, Naushin S, Wadhwa S, Tyagi N, Poojary M, Scaria V*, Sivasubbu S*.

High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing.

PLoS One. 2021 Feb 17;16(2):e0247115. doi: 10.1371/journal.pone.0247115.

[122] Philomina J B, Jolly B, John N, Bhoyar RC, Majeed N, Senthivel V, Cp F, Rophina M, Vasudevan B, Imran M, Viswanathan P, Arvinden VR, Joseph A, Divakar MK, Nair PR, Shamnath A, Kumar PJ, Jain A, Geetha P, Bajaj A, Mathew S, Gupta V, Agrawal SJ, Scaria V*, Sivasubbu S*, Radhakrishnan C*.

Genomic survey of SARS-CoV-2 vaccine breakthrough infections in healthcare workers from Kerala, India.

J Infect. 2021 May 25;83(2):237–79. doi: 10.1016/j.jinf.2021.05.018.

[121] Kohli S, Gulati P, Narang A, Maini J, Shamsudheen KV, Pandey R, Scaria V, Sivasubbu S, Brahmachari V.

Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: Correlation with its unique phenotypes.

Genomics. 2021 Jul;113(4):2483-2494. doi: 10.1016/j.ygeno.2021.05.014.

[120] Rani PR, Imran M, Lakshmi JV, Jolly B, Jain A, Surekha A, Senthivel V, Chandrasekhar P, Divakar MK, Srinivasulu D, Bhoyar RC, Vanaja PR, Scaria V*, Sivasubbu S*.

Symptomatic reinfection of SARS-CoV-2 with spike protein variant N440K associated with immune escape.

J Med Virol. 2021 Jul;93(7):4163-4165. doi: 10.1002/jmv.26997.

[119] Radhakrishnan C, Divakar MK, Jain A, Viswanathan P, Bhoyar RC, Jolly B, Imran M, Sharma D, Rophina M, Ranjan G, Sehgal P, Jose BP, Raman RV, Kesavan TN, George K, Mathew S, Poovullathil JK, Keeriyatt Govindan SK, Nair PR, Vadekkandiyil S, Gladson V, Mohan M, Parambath FC, Mangla M, Shamnath A; Indian CoV2 Genomics & Genetic Epidemiology (IndiCovGEN) Consortium, Sivasubbu S*, Scaria V*.

Initial Insights Into the Genetic Epidemiology of SARS-CoV-2 Isolates From Kerala Suggest Local Spread From Limited Introductions.

Front Genet. 2021 Mar 17;12:630542. doi: 10.3389/fgene.2021.630542.

[118] Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S*.

Functional long non-coding and circular RNAs in zebrafish.

Brief Funct Genomics. 2021 Mar 23:elab014. doi: 10.1093/bfgp/elab014.

[117] Singh MK, Jayarajan R, Varshney S, Upadrasta S, Singh A, Yadav R, Scaria V, Sengupta S, Shanmugam D, Shalimar, Sivasubbu S, Gandotra S, Sachidanandan C.

Chronic systemic exposure to IL6 leads to deregulation of glycolysis and fat accumulation in the zebrafish liver.

Biochim Biophys Acta Mol Cell Biol Lipids. 2021 May;1866(5):158905. doi: 10.1016/j.bbalip.2021.158905.

[116] Vatsyayan A, Sharma P, Gupta S, Sandhu S, Venu SL, Sharma V, Badaoui B, Azedine K, Youssef S, Rajab A, Fayez A, Madinur S, Ranawat A, Pandhare K, Ramachandran S, Sivasubbu S, Scaria V.

DALIA- a comprehensive resource of Disease Alleles in Arab population.

PLoS One. 2021 Jan 13;16(1):e0244567. doi: 10.1371/journal.pone.0244567.

[115] Singh P, Chakraborty R, Marwal R, Radhakrishan VS, Bhaskar AK, Vashisht H, Dhar MS, Pradhan S, Ranjan G, Imran M, Raj A, Sharma U, Singh P, Lall H, Dutta M, Garg P, Ray A, Dash D, Sivasubbu S, Gogia H, Madan P, Kabra S, Singh SK, Agrawal A, Rakshit P, Kumar P, Sengupta S.

A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry.

J Proteins Proteom. 2020 Aug 31:1-7. doi: 10.1007/s42485-020-00044-9.

[114] Govindaraj GM, Ramya U, Raj R, Athulya EP, Jain A, Scaria V, Jayakrishnan MP, Sivasubbu S, Dhanasooraj D, Ajithkumar VT, Dongre AR, Krishnakumar P.

Parental Experience of Hematopoietic Stem Cell Transplantation for Children with Primary Immune Deficiency Disorders.

Indian J Pediatr. 2021 Apr;88(4):370-371. doi: 10.1007/s12098-020-03541-3.

[113] Yadav SP, Thakkar D, Bhoyar RC, Jain A, Wadhwa T, Imran M, Jolly B, Divakar MK, Kapoor R, Rastogi N, Sharma D, Sehgal P, Ranjan G, Sivasubbu S, Sarma S, Scaria V. Asymptomatic reactivation of SARS-CoV-2 in a child with neuroblastoma characterised by whole genome sequencing.

IDCases. 2021;23:e01018. doi: 10.1016/j.idcr.2020.e01018.

[112] Abhinav Jain, Mercy Rophina, Saurabh Mahajan, Bhavya Balaji Krishnan, Manasa Sharma, Sreya Mandal, Teresa Fernandez, Sumayra Sultanji, Bani Jolly, Samatha Mathew, Sridhar Sivasubbu, Vinod Scaria.

Analysis of the potential impact of genomic variants in global SARS-CoV-2 genomes on molecular diagnostic assays.

Int J Infect Dis. 2021 Jan;102:460-462. doi: 10.1016/j.ijid.2020.10.086.

2020

[111] Ichino N, Serres MR, Urban RM, Urban MD, Treichel AJ, Schaefbauer KJ, Greif LE, Varshney GK, Skuster KJ, McNulty MS, Daby CL, Wang Y, Liao HK, El-Rass S, Ding Y, Liu W, Anderson JL, Wishman MD, Sabharwal A, Schimmenti LA, Sivasubbu S, Balciunas D, Hammerschmidt M, Farber SA, Wen XY, Xu X, McGrail M, Essner JJ, Burgess SM, Clark KJ, Ekker SC.

Building the vertebrate codex using the gene breaking protein trap library.

Elife. 2020 Aug 11;9:e54572. doi: 10.7554/eLife.54572.

[110] Gupta V, Bhoyar RC, Jain A, Srivastava S, Upadhayay R, Imran M, Jolly B, Divakar MK, Sharma D, Sehgal P, Ranjan G, Gupta R, Scaria V*, Sivasubbu S*.

Asymptomatic reinfection in two healthcare workers from India with genetically distinct SARS-CoV-2.

Clin Infect Dis. 2020 Sep 23:ciaa1451. doi: 10.1093/cid/ciaa1451.

[109] Raja DA, Subramaniam Y, Aggarwal A, Gotherwal V, Babu A, Tanwar J, Motiani RK, Sivasubbu S, Gokhale RS, Natarajan VT.

Histone variant dictates fate biasing of neural crest cells to melanocyte lineage.

Development. 2020;147(5):dev182576. Published 2020 Mar 12. doi:10.1242/dev.182576

[108] Raja DA, Gotherwal V, Burse SA, Subramaniam YJ, Sultan F, Vats A, Gautam H, Sharma B, Sharma S, Singh A, Sivasubbu S, Gokhale RS, Natarajan VT.

pH-controlled histone acetylation amplifies melanocyte differentiation downstream of MITF.

EMBO Rep. 2020;21(1):e48333. doi:10.15252/embr.201948333

[107] Govindaraj GM, Jain A, Peethambaran G, Bhoyar RC, Vellarikkal SK, Ganapati A, Sandhya P, Edavazhippurath A, Dhanasooraj D, Puthenpurayil JM, Chakkiyar K, Mishra A, Batra A, Punnen A, Kumar S, Sivasubbu S, Scaria V.

Spectrum of clinical features and genetic variants in mevalonate kinase (MVK) gene of South Indian families suffering from Hyperimmunoglobulin D Syndrome.

PLoS One. 2020 Aug 21;15(8):e0237999. doi: 10.1371/journal.pone.0237999.

[106] Singh P, Chakraborty R, Marwal R, Radhakrishan VS, Bhaskar AK, Vashisht H, Dhar MS, Pradhan S, Ranjan G, Imran M, Raj A, Sharma U, Singh P, Lall H, Dutta M, Garg P, Ray A, Dash D, Sivasubbu S, Gogia H, Madan P, Kabra S, Singh SK, Agrawal A, Rakshit P, Kumar P, Sengupta S.

A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry.

J Proteins Proteom. 2020 Aug 31:1-7. doi: 10.1007/s42485-020-00044-9.

[105] Sharma D, Sandhya P, Vellarikkal SK, Surin AK, Jayarajan R, Verma A, Kumar A, Ravi R, Danda D, Sivasubbu S, Scaria V.

Saliva microbiome in primary Sjögren's syndrome reveals distinct set of disease-associated microbes.

Oral Dis. 2020 Mar;26(2):295-301. doi: 10.1111/odi.13191. Epub 2020 Jan 10.

[104] Tanwar VS, Ghosh S, Sati S, Ghose S, Kaur L, Kumar KA, Shamsudheen KV, Patowary A, Singh M, Jyothi V, Kommineni P, Sivasubbu S, Scaria V, Raghunath M, Mishra R, Chandak GR, Sengupta S.

Maternal vitamin B12 deficiency in rats alters DNA methylation in metabolically important genes in their offspring.

Mol Cell Biochem. 2020;468(1-2):83-96. doi:10.1007/s11010-020-03713-x

[103] Chakraborty S, Vellarikkal SK, Sivasubbu S, Roy SS, Tandon N, Bharadwaj D.

Role of Tmem163 in zinc-regulated insulin storage of MIN6 cells: Functional exploration of an Indian type 2 diabetes GWAS associated gene.

Biochem Biophys Res Commun. 2020;522(4):1022-1029. doi:10.1016/j.bbrc.2019.11.117

[102] Jagtap U, Sivadas A, Basu S, Verma A, Sivasubbu S, Scaria V, Sachidanandan C.

A Temporal Map of Gene Expression Pattern During Zebrafish Liver Regeneration.

Zebrafish. 2020;17(1):1-10. doi:10.1089/zeb.2019.1790

[101] Ghose S, Ghosh S, Tanwar VS, Tolani P, Kutum R, Sharma A, Bhardwaj N, Shamsudheen KV, Verma A, Jayarajan R, Dash D, Sivasubbu S, Scaria V, Seth S, Sengupta S.

Investigating Coronary Artery Disease methylome through targeted bisulfite sequencing.

Gene. 2019;721:144107. doi:10.1016/j.gene.2019.144107

2019

[100] The GUaRDIAN Consortium, Sridhar Sivasubbu*, Vinod Scaria*.

Genomics Of Rare Genetic Diseases – Experiences From India.

BMC Human Genomics 2019 Sep 25;14(1):52

[99] Sharma D, Sehgal P, Mathew S, Vellarikkal SK, Singh AR, Kapoor S, Jayarajan R, Scaria V*, Sivasubbu S*.

A genome-wide map of circular RNAs in adult zebrafish.

Sci Rep. 2019 Mar 5;9(1):3432. doi: 10.1038/s41598-019-39977-7.

[98] Mathew S, Sivadas A, Sehgal P, Kaushik K, Vellarikkal SK, Scaria V*, Sivasubbu S*.

Methods to Study Long Noncoding RNA Expression and Dynamics in Zebrafish Using RNA Sequencing.

Methods Mol Biol. 2019;1912:77-110. doi:10.1007/978-1-4939-8982-9_4.

[97] Biswas A, Raza A, Das S, Kapoor M, Jayarajan R, Verma A, Shamsudheen KV, Murry B, Seth S, Bhargava B, Scaria V, Sivasubbu S, Rao VR.

Loss of function mutation in the P2X7, a ligand-gated ion channel gene associated with hypertrophic cardiomyopathy.

Purinergic Signal. 2019 May 31. doi: 10.1007/s11302-019-09660-7.

[96] Thottath J, Vellarikkal SK, Jayarajan R, Verma A, Manamel M, Singh A,

Rajendran VR, Sivasubbu S, Scaria V.

A novel cathepsin D mutation in 2 siblings with late infantile neuronal ceroid lipofuscinosis.

Neurol Genet. 2019 Apr 11;5(3):e302. doi: 10.1212/NXG.0000000000000302. eCollection 2019 Jun.

[95] Sharma D, Sehgal P, Hariprakash J, Sivasubbu S, Scaria V.

Methods for Annotation and Validation of Circular RNAs from RNAseq Data.

Methods Mol Biol. 2019;1912:55-76. doi: 10.1007/978-1-4939-8982-9_3.

[94] Bhoyar RC, Jadhao AG, Sabharwal A, Ranjan G, Sivasubbu S, Pinelli C. Knockdown of calcium-binding calb2a and calb2b genes indicates the key regulator of the early development of the zebrafish, Danio rerio.

Brain Struct Funct. 2019 Mar;224(2):627-642. doi: 10.1007/s00429-018-1797-8.

2018

[93] Hariprakash JM, Vellarikkal SK, Verma A, Ranawat AS, Jayarajan R, Ravi R, Kumar A, Dixit V, Sivadas A, Kashyap AK, Senthivel V, Sehgal P, Mahadevan V, Scaria V*, Sivasubbu S*.

SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes.

Database (Oxford). 2018 Jan 1;2018:1-10. doi: 10.1093/database/bay080. PubMed PMID: 30184194; PubMed Central PMCID: PMC6146123.

[92] Vellarikkal SK, Jayarajan R, Verma A, Ravi R, Senthivel V, Kumar A, Saini L, Gulati S, Lal M, Mathur A, Chhetri MK, Faruq M, Scaria V*, Sivasubbu S*.

A founder mutation MLC1 c.736delA associated with megalencephalic leukoencephalopathy with subcortical cysts-1in north Indian kindred.

Clinical Genetics. 2018, Aug;94(2):271-273. doi: 10.1111/cge.13251

[91] Sabharwal A, Sharma D, Vellarikkal SK, Jayarajan R, Verma A, Senthivel V,

Scaria V*, Sivasubbu S*.

Organellar transcriptome sequencing reveals mitochondrial localization of nuclear encoded transcripts.

Mitochondrion. 2018 Feb 24. pii:S1567-7249(17)30106-X.

[90] Kaushik K, Sivadas A, Vellarikkal SK, Verma A, Jayarajan R, Pandey S, Sethi T, Maiti, Scaria V*, Sivasubbu S*

RNA secondary structure profiling in zebrafish reveals unique regulatory features

BMC Genomics. 2018 Feb 15;19(1):147

[89] Yenamandra VK, Vellarikkal SK, Chowdhury MR, Jayarajan R, Verma A, Scaria V, Sivasubbu S, Ray SB, Dinda AK, Kabra M, Sharma VK, Sethuraman G.

Genotype-Phenotype Correlations of Dystrophic Epidermolysis Bullosa in India: Experience from a Tertiary Care Centre.

Acta Derm Venereol. 2018 Oct 10;98(9):873-879.

[88] Virmani N, Vellarikkal SK, Verma A, Jayarajan R, Sakhiya J, Desai C, Sivasubbu S, Scaria V.

Whole exome sequencing in a multi-generation family from India reveals a genetic variation c.10C>T (p.Gln4Ter) in keratin 5 gene associated with Dowling-Degos disease.

Indian J Dermatol Venereol Leprol. 2018 Mar 29. doi:10.4103/ijdvl.IJDVL 268_17.

[87] Ramasamy S, Sharma S, Iyengar BR, Vellarikkal SK, Sivasubbu S, Maiti S, Pillai B.

Identification of novel circadian transcripts in the zebrafish retina.

J Exp Biol. 2018 Nov 16. pii: jeb.192195.

[86] Bhambri A, Dhaunta N, Patel SS, Hardikar M, Bhatt A, Srikakulam N, Shridhar S, Vellarikkal S, Pandey R, Jayarajan R, Verma A, Kumar V, Gautam P, Khanna Y, Khan JA, Fromm B, Peterson KJ, Scaria V, Sivasubbu S, Pillai B.

Large scale changes in the transcriptome of Eisenia fetida during regeneration.

PLoS One. 2018 Sep 27;13(9):e0204234.

[85] Nahar S, Sehgal P, Azhar M, Rai M, Singh A, Sivasubbu S, Chakraborty D, Maiti S.

A G-quadruplex motif at the 3' end of sgRNAs improves CRISPR-Cas9 based genome editing efficiency.

Chem Commun (Camb). 2018 Mar 7;54(19):2377-2380.

[84] Motiani RK, Tanwar J, Raja DA, Vashisht A, Khanna S, Sharma S, Srivastava S,Sivasubbu S, Natarajan VT, Gokhale RS.

STIM1 activation of adenylyl cyclase 6 connects Ca(2+) and cAMP signaling during melanogenesis.

EMBO J. 2018 Mar 1;37(5). pii: e97597.

[83] Hariprakash JM, Vellarikkal SK, Keechilat P, Verma A, Jayarajan R, Dixit V, Ravi R, Senthivel V, Kumar A, Sehgal P, Sonakar AK, Ambawat S, Giri AK, Philip A, Sivadas A, Faruq M, Bharadwaj D, Sivasubbu S*, Scaria V*.

Pharmacogenetic landscape of DPYD variants in south Asian populations by integration of genome-scale data.

Pharmacogenomics. 2018 Feb;19(3):227-241.

[82] Biswas A, Das S, Kapoor M, Shamsudheen KV, Jayarajan R, Verma A, Seth S, Bhargava B, Scaria V, Sivasubbu S, Rao VR.

Familial hypertrophic cardiomyopathy - Identification of cause and risk stratification through exome sequencing.

Gene. 2018 Mar 20. pii: S0378-1119(18)30306-8

[81] Mahajan R, Vellarikkal SK, Handa S, Verma A, Jayarajan R, Kumar A, De D, Kaur J, Panigrahi I, VSl V, Sivasubbu S*, Scaria V*.

Utility of whole exome sequencing in detecting novel compound heterozygous mutations in COL7A1 among families with severe recessive Dystrophic Epidermolysis Bullosa in India - implications on diagnosis, prognosis and prenatal testing.

J Eur Acad Dermatol Venereol. 2018 Mar 6. doi: 10.1111/jdv.14909.

2017

[80] Ramkumar A, Murthy D, Raja DA, Singh A, Krishnan A, Khanna S, Vats A, Thukral L, Sharma P, Sivasubbu S, Rani R, Natarajan VT, Gokhale RS.

Classical autophagy proteins LC3B and ATG4B facilitate melanosome movement on cytoskeletal tracks.

Autophagy. 2017 Aug 3;13(8):1331-1347.

[79] Goyal N, Sivadas A, Shamsudheen KV, Jayarajan R, Verma A, Sivasubbu S, Scaria V, Datta M.

RNA sequencing of db/db mice liver identifies lncRNA H19 as a key regulator of gluconeogenesis and hepatic glucose output.

Sci Rep. 2017 Aug 16;7(1):8312

[78] Govindaraj GM, Karuthedath Vellarikkal S, Jayarajan R, Ravi R, Verma A, Chakkiyar K, Jayakrishnan MP, Arakkal R, Raj R, Kunnaruvath R, Sivasubbu S*, Scaria V*.

Case Report: Whole exome sequencing identifies variation c.2308G>A p.E770K in RAG1 associated with B- T- NK+ severe combined immunodeficiency.

F1000Res. 2016 Oct 18 [revised 2017 Jan 1]; 5:2532.

[77] Rawat A, Karuthedath Vellarikkal S, Verma A, Jayarajan R, Gupta A, Singh S, Chopra A, Kumar R, Scaria V*, Sivasubbu S*.

Case Report: Whole exome sequencing identifies a novel frameshift insertion c.1325dupT (p.F442fsX2) in the tyrosine kinase domain of BTK gene in a young Indian individual with X-linked agammaglobulinemia.

Version 2. F1000Res. 2016 Nov 14 [revised 2017 Jan 1]; 5:2667.

[76] Yenamandra VK, Shamsudheen KV, Madhumita RC, Jayarajan R, Verma A, Scaria V, Sivasubbu S, Kabra M, Sharma VK and Sethuraman G

Autosomal recessive epidermolysis bullosa simplex: report of three cases from India

Clinical and Experimental Dermatology (2017) 42, pp791–810 doi: 10.1111/ced.13182

[75] Yenamandra VK, Vellarikkal SK, Kumar M, Chowdhury MR, Jayarajan R, Verma A, Scaria V, Sivasubbu S, Ray SB, Dinda AK, Kabra M, Kaur P, Sharma VK, Sethuraman G.

Application of Whole Exome Sequencing in Elucidating the Phenotype and Genotype Spectrum of Junctional Epidermolysis Bullosa: A Preliminary Experience of a Tertiary Care Centre in India.

J Dermatol Sci, 2017. Apr;86(1):30-36

[74] Sandhya P, Vellarikkal SK, Nair A, Ravi R, Mathew J, Jayarajan R, Kumar A, Verma A, Sivadas A, Danda D, Sivasubbu S*, Scaria V*

Egyptian tale from India - application of whole-exome sequencing in diagnosis of atypical Familial Mediterranean Fever.

Int J Rheum Dis, 2017. doi: 10.1111/1756-185X.13042

[73] Bhoyar RC, Jadhao AG, Sivasubbu S, Singh AR, Sabharwal A, Palande NV, Biswas S.

Neuroanatomical demonstration of calbindin 2a- and calbindin 2b-like calcium binding proteins in the early embryonic development of zebrafish: mRNA study.

Int J Dev Neurosci. 2017 Aug;60:26-33

[72] Yenamandra VK, Moss C, Sreenivas V, Khan M, Sivasubbu S, Sharma VK, Sethuraman G.

Development of a Clinical Diagnostic Matrix for characterising Inherited Epidermolysis Bullosa.

British J Dermatol. (2017) Accepted

[71] Nathiga Nambi KS, Abdul Majeed S, Taju G, Sivasubbu S, Sarath Babu V, Sahul Hameed AS.

Effects of nicotine on zebrafish: A comparative response between a newly established gill cell line and whole gills.

Comp Biochem Physiol C Toxicol Pharmacol. 2017 May;195:68-77

2016

[70] 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

[69] Karuthedath Vellarikkal S, Jayarajan R, Verma A, Nair S, Ravi R, Senthivel V, Sivasubbu S*, Scaria V*.

Case Report: Whole exome sequencing reveals a novel frameshift deletion mutation p.G2254fs in COL7A1 associated with autosomal recessive dystrophic epidermolysis bullosa.

F1000Res. 2016 May 17;5: 900.

[68] 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 Apr 4;11(4):e0153001

[67] Vij S, Kuhl H, Kuznetsova IS, Komissarov A, Yurchenko AA, Van Heusden P, Singh S, Thevasagayam NM, Prakki SR, Purushothaman K, Saju JM, Jiang J, Mbandi SK, Jonas M, Hin Yan Tong A, Mwangi S, Lau D, Ngoh SY, Liew WC, Shen X, Hon LS, Drake JP, Boitano M, Hall R, Chin CS, Lachumanan R, Korlach J, Trifonov V, Kabilov M, Tupikin A, Green D, Moxon S, Garvin T, Sedlazeck FJ, Vurture GW, Gopalapillai G, Kumar Katneni V, Noble TH, Scaria V, Sivasubbu S, Jerry DR, O'Brien SJ, Schatz MC, Dalmay T, Turner SW, Lok S, Christoffels A, Orbán L.

Chromosomal-Level Assembly of the Asian Seabass Genome Using Long Sequence Reads and Multi-layered Scaffolding.

PLoS Genetics. 2016 Apr 15;12(4):e1005954.

[66] Pawar N, Gireesh-Babu P, Sabnis S, Rasal K, Murthy R, Zaidi SG, Sivasubbu S, Chaudhari A.

Development of a fluorescent transgenic zebrafish biosensor for sensing aquatic heavy metal pollution.

Transgenic Res. 2016 Oct;25(5):617-27.

[65] 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. 2016 Apr;30(4):695-7. doi: 10.1111/jdv.12983

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] 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.

[58] 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

[57] 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.

[56] 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

[55] 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.

[54] 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

[53] 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

[52] 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

[51] 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.

[50] 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.

[49] 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

[48] 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.

[47] Sivasubbu S*, Sachidanandan C, Scaria V*.

Time for the zebrafish ENCODE.

J Genet. 2013 Dec;92(3):695-701.

[46] 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.

[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 Multidrug-Resistant Mycobacterium tuberculosis Clinical Isolate OSDD515, Belonging to the Uganda I Genotype.

Genome Announc. 2013 Nov 21;1(6). pii: e00750-13.

[44] 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.

[43] 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.

(This article describes the first human genome from Malaysia)

[42] 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.

[41] 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.

[40] 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.

(This article describes the first wild zebrafish genome)

Highlighted by the journal Cell in the Leading Edge Analysis (Cell 139, Nov 25, 2009)

[39] 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.

[38] 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

[37] Lalwani MK, Sharma M, Singh AR, Chauhan RK, Patowary A, Singh N, Scaria V*, Sivasubbu S*.

Reverse genetics screen in zebrafish identifies a role of miR-142a-3p in vascular development and integrity.

PLoS One. 2012;7(12):e52588.

[36] 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;40(18):8965-78.

[35] Goswami R, Singh A, Gupta N; Indian Genome Variation Consortium^, Rani R.

Presence of strong association of the major histocompatibility complex (MHC) class I allele HLA-A*26:01 with idiopathic hypoparathyroidism.

J Clin Endocrinol Metab. 2012 Sep;97(9):E1820-4.

(^Co-author of Consortia)

[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] 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.

[32] 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.

(This article describes the first human genome from India)

[31] 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.

[30] 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.

[29] 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.

[28] 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.

[27] 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.

[26] 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.

2011

[25] Ding Y, Sun X, Huang W, Hoage T, Redfield M, Kushwaha S, Sivasubbu S, Lin X, Ekker S, Xu X.

Haploinsufficiency of target of rapamycin attenuates cardiomyopathies in adult zebrafish.

Circ Res. 2011 Sep 2;109(6):658-69.

[24] 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.

Nat Methods. 2011 Jun;8(6):506-15.

(This article describes the first conditional mutants in vertebrates outside the mouse model)

Highlighted in News and Views, Nature Methods, 8, 466, 2011.

[23] 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.

(This article describes the first human genome from Sri Lanka)

2010

[22] Aggarwal S, Negi S, Jha P, Singh PK, Stobdan T, Pasha MA, Ghosh S, Agrawal A; Indian Genome Variation Consortium^, Prasher B, Mukerji M.

EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda.

Proc Natl Acad Sci U S A. 2010 Nov2;107(44):18961-6.

(^Co-author of Consortia)

[21] Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, Patowary A,

Purkanti R, Lalwani M, Singh AR, Chauhan R, Singh N, Bhardwaj A, Scaria V*, Sivasubbu S*.

FishMap Zv8 update--a genomic regulatory map of zebrafish.

Zebrafish. 2010 Jun;7(2):179-80.

2009

[20] 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

[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 Dec 16;47(50):13179-88.

[18] Indian Genome Variation Consortium^.

Genetic landscape of the people of India: a canvas for disease gene exploration.

J Genet. 2008 Apr;87(1):3-20. (^Co-author of Consortia)

[17] Meli R, Prasad A, Patowary A, Lalwani MK, Maini J, Sharma M, Singh AR, Kumar G, Jadhav V, Scaria V*, Sivasubbu S*.

FishMap: a community resource for zebrafish genomics.

Zebrafish. 2008 Summer;5(2):125-30.

2007

[16] Sivasubbu S, Balciunas D, Amsterdam A, Ekker SC.

Insertional mutagenesis strategies in zebrafish.

Genome Biol. 2007;8 Suppl 1:S9.

2006

[15] Pickart MA, Klee EW, Nielsen AL, Sivasubbu S, Mendenhall EM, Bill BR, Chen E, Eckfeldt CE, Knowlton M, Robu ME, Larson JD, Deng Y, Schimmenti LA, Ellis LB, Verfaillie CM, Hammerschmidt M, Farber SA, Ekker SC.

Genome-wide reverse genetics framework to identify novel functions of the vertebrate secretome.

PLoS One. 2006 Dec 20;1:e104.

[14] Balciunas D, Wangensteen KJ, Wilber A, Bell J, Geurts A, Sivasubbu S, Wang X, Hackett PB, Largaespada DA, McIvor RS, Ekker SC.

Harnessing a high cargo-capacity transposon for genetic applications in vertebrates.

PLoS Genet. 2006 Nov 10;2(11):e169.

[13] Sivasubbu S, Balciunas D, Davidson AE, Pickart MA, Hermanson SB, Wangensteen KJ, Wolbrink DC, Ekker SC.

Gene-breaking transposon mutagenesis reveals an essential role for histone H2afza in zebrafish larval development.

Mech Dev. 2006 Jul;123(7):513-29.

(This article describes the first transposon mediated insertional mutant in zebrafish)

2004

[12] Hermanson S, Davidson AE, Sivasubbu S, Balciunas D, Ekker SC.

Sleeping Beauty transposon for efficient gene delivery.

Methods Cell Biol. 2004;77:349-62.

[11] Pickart MA, Sivasubbu S, Nielsen AL, Shriram S, King RA, Ekker SC.

Functional genomics tools for the analysis of zebrafish pigment.

Pigment Cell Res. 2004 Oct;17(5):461-70.

[10] Balciunas D, Davidson AE, Sivasubbu S, Hermanson SB, Welle Z, Ekker SC.

Enhancer trapping in zebrafish using the Sleeping Beauty transposon.

BMC Genomics. 2004 Sep 3;5(1):62.

[09] Haniffa, M. A., Sridhar, S and Nagarajan, M.

Induction of triploidy and tetraploidy in stinging catfish, Heteropneustes fossilis (Bloch), using heat shock.

Aquaculture Research. 2004. 35(10): 937-942.

[08] 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.

2003 and prior

[07] Davidson AE, Balciunas D, Mohn D, Shaffer J, Hermanson S, Sivasubbu S, Cliff MP, Hackett PB, Ekker SC.

Efficient gene delivery and gene expression in zebrafish using the Sleeping Beauty transposon.

Dev Biol. 2003 Nov15;263(2):191-202.

[06] 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.

[05] 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.

[04] Haniffa, M.A., Jesu Arockia Raj, A and Sridhar, S.

Weaning diet for striped murrel Channa Straitus.

Fisheries Technology. 1999. 36 (2):116-119.

[03] 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.

[02] 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.

[01] 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.

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