(*indicates Corresponding Author) 2021 [129] 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.
[128] 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.
[127] 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. [COVID19] (INSACOG Consortia co-author)
[126] 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. [COVID19]
[125] 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
[124] 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.
[123] 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. [COVID19]
[122] 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. [COVID19]
[121] 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. [COVID19]
[120] 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.
[119] 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. [COVID19]
[118] 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. [COVID19]
[117] 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.
[116] 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.
[115] 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.
[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. [COVID19]
[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. [COVID19]
[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. [COVID19]
[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. 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] 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*. [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. |
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