Publications

2021


[192] Rophina M, Pandhare K, Shamnath A, Imran M, Jolly B and Scaria V

ESC - a comprehensive resource for SARS-CoV-2 immune escape variants.

Nucleic Acids Research (2021) Accepted [COVID-19]


[191] Sharma D, Sehgal P, Sivasubbu S, Scaria V,

A genome-wide circular RNA transcriptome in Rat,

Biology Methods and Protocols, 2021;, bpab016, https://doi.org/10.1093/biomethods/bpab016


[190] Devassikutty, FM, Jain A, Edavazhippurath A, Joseph MC, Peedikayil MNT, Scaria V, Sandhya P, and Govindaraj GM.

X-Linked Agammaglobulinemia and COVID-19: Two Case Reports and Review of Literature

Pediatric Allergy, Immunology, and Pulmonology.Sep 2021.115-118.http://doi.org/10.1089/ped.2021.0002 [COVID-19]


[189] 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. Epub ahead of print. PMID: 34180064.


[188] Kesharwani D, Kumar A, Poojary M, Scaria V, Datta M.

RNA Sequencing reveals potential interacting networks between the altered transcriptome and ncRNome in the skeletal muscle of diabetic mice.

Biosci Rep. 2021 Jun 30:BSR20210495. doi: 10.1042/BSR20210495. Epub ahead of print. PMID: 34190986.


[187] Roja Rani P, Imran M, Vijaya Lakshmi J, Jolly B, Afsar S, Jain A, Divakar MK, Suresh P, Sharma D, Rajesh N, Bhoyar RC, Ankaiah D, Shanthi Kumari S, Ranjan G, Anitha Lavanya V, Rophina M, Umadevi S, Sehgal P, Renuka Devi A, Surekha A, Chandra Sekhar P, Hymavathy R, Vanaja PR, Scaria V, Sivasubbu S.

Insights from Genomes and Genetic Epidemiology of SARS-CoV-2 isolates from the state of Andhra Pradesh.

Epidemiology and Infection. 2021;:1–11. [COVID-19]


[186] Mittal G, Anu RI, Vatsyayan A, Pandhare K, Scaria V

MUSTARD - a comprehensive resource of Mutation Specific Therapies in Cancer

Database (Oxford) 2021 Accepted


[185] 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 Jun 18. doi: 10.2217/pgs-2021-0028. Epub ahead of print. PMID: 34142560. [COVID-19]


[184] Cotsapas C, Saarela J, Farmer JR, Scaria V, Abraham RS.

Do monogenic inborn errors of immunity cause susceptibility to severe COVID-19?

J Clin Invest. 2021 Jun 1:149459. doi: 10.1172/JCI149459 . [COVID-19]


[183] Philomina JB, Jolly B, John N, Bhoyar RC, Majeed N, Senthivel V, P FC, 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 24:S0163-4453(21)00260-7. doi: 10.1016/j.jinf.2021.05.018. [COVID-19]


[182] 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 May 19:S0888-7543(21)00187-7. doi: 10.1016/j.ygeno.2021.05.014. Epub ahead of print. PMID: 34022346.


[181] 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 Apr 5. doi: 10.1002/jmv.26997. Epub ahead of print. PMID: 33818797. [COVID-19]


[180] 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. PMID: 33815467; PMCID: PMC8010186. [COVID-19]


[179] Sharma P, Jain A and Scaria V*

Genetic landscape of rare autoinflammatory disease variants in Qatar and Middle Eastern populations through the integration of whole-genome and exome datasets

Front. Genet.(2021) Accepted


[178] Ranjan G, Sehgal P, Sharma D, Scaria V, Sivasubbu S

Functional long non-coding and circular RNAs in zebrafish

Briefings in Functional Genomics, elab014, https://doi.org/10.1093/bfgp/elab014


[177] Jain, A, Sharma D, Bajaj, A, Gupta V, Scaria V

Founder variants and population genomes—Toward precision medicine

Advances in Genetics (Academic Press) (2021) Accepted


[176] Jolly B, Scaria V

Computational Analysis and Phylogenetic clustering of SARS-nCov-2 Genomes

Bio-protocol (2021) Accepted [COVID-19]


[175]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. PMID: 33596239; PMCID: PMC7888613. [COVID-19]


[174] Govindaraj GM, Ramya U, Ashraf TP, Raj R, Scaria V

Hematopoietic Stem Cell Transplantation for Children With Inborn Errors of Immunity

Indian Pediatrics 58 (2), 179


[173] Rajan R, Garg K, Saini A, Kumar M, Binukumar BK, Scaria V, Aggarwal R, Gupta A, Vishnu VY, Garg A, Singh MB, Bhatia R, Srivastava AK, Srivastava P, Singh M

Pallidal deep brain stimulation for KMT2B related dystonia in an Indian patient

Annals of Indian Academy of Neurology (2021) Accepted


[172] Singh MK, Jayarajan J, 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

Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids (2021)


[171] Vatsyayan A, Scaria V

Understanding genetic epidemiology and population disparities of inherited blood cancer syndromes from integrative analysis of population genomics datasets

Pediatric Hematology Oncology Journal (2021)


[170] Vatsyayan V, 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)


[169] Jain A, Bhoyar RC,Pandhare K, Mishra A, Sharma D,Imran M, Senthivel V,Divakar1 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, Senthil Kumar N, Vanlallawma A, Sarma RJ, Chhakchhuak L, Kalyanaraman S,Mahadevan R, Kandasamy S, Pabitha BM, Rajagopal RE, Ramya E, Nirmala Devi P, Bajaj A, Gupta V, Mathew S,Goswami SG, Mangla M, Prakash S, Joshi K, Meyakumla, Sreedevi S, Gajjar D, Ronibala Soraisham, Yadav R, Silla Devi Y, Gupta A, Mukerji M, Ramalingam S, Binukumar BK, Scaria V,Sivasubbu S

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

Nucleic Acids Research (2020) doi: 10.1093/nar/gkaa923


[168]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 suggests a founder repeat expansion mutation in the SAMD12 gene

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


[167] Jalali S, Singh A, Scaria V and Maiti S

Genome-wide computational analysis and validation of potential long noncoding RNA mediated DNA-DNA:RNA triplexes in the human genome

Methods in Molecular Biology (2021) 2254:61-71. doi: 10.1007/978-1-0716-1158-6_5.


[166] Jain A, Rophina M, Mahajan S, Krishnan BB, Sharma M, Mandal S, Fernandez T, Sultanji S, Mathew S, Sivasubbu S, Scaria V

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

International Journal of Infectious Diseases (2021) https://doi.org/10.1016/j.ijid.2020.10.086 [COVID-19]


[165] 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), e01018, https://doi.org/10.1016/j.idcr.2020.e01018 . [COVID-19]

2020

[164]Govindaraj GM, Krishnakumar P, Scaria V, Athulya E, Ajithkumar VT, Dongre AR.

Building on an Ad Hoc Covid-19 Response to Enhance Community-based Care for Vulnerable Children in Kerala, India.

NEJM Catal Innov Care Deliv. (2020) doi: 10.1056/CAT.20.0543. [COVID-19]


[163] Bishnoi A, Jamwal M, Das R, Scaria V, Vishwajeet V, De D, Saikia UN, Mahajan R.

Clericuzio-type poikiloderma with neutropenia in a patient from India.

Am J Med Genet A. 2020 Oct 27. doi: 10.1002/ajmg.a.61943. Online ahead of print.


[162] 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. (2020) Oct 23. doi: 10.1007/s12098-020-03541-3. Online ahead of print.


[161] Brahmbhatt HD, Gupta R, Gupta A, Rastogi S, Misri R, Mobeen A, Ghosh A, Kothari P, Sitaniya S, Scaria V, Singh A

Long non-coding RNA MALAT1 suppresses miR-211 to confer protection from UV-mediated DNA damage in vitiligo epidermis by upregulating SIRT1

British Journal of Dermatology (2020) https://doi.org/10.1111/bjd.19666


[160] 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.

Clinical Infectious Diseases (2020) ciaa1451, https://doi.org/10.1093/cid/ciaa1451 [COVID-19]


[159] Banu S, Jolly B, Mukherjee P, Singh P, Khan S, Zaveri L, Shambhavi S, Gaur N, Reddy S, Kaveri K, Srinivasan S, Gopal DR, Siva AB, Thangaraj K, Tallapaka KB, Mishra RK, Scaria V, Sowpati DT

A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates

Open Forum Infectious Diseases, (2020), ofaa434, https://doi.org/10.1093/ofid/ofaa434 [COVID-19]


[158] Govindaraj GM, Jain A, Peethambaran G, Bhoyar R, 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) Accepted


[157] Mhaske A, Dileep KV, Kumar M, Poojary M, Pandhare K, Zhang KYJ, Scaria V, and Binukumar BK (2020)

ATP7A Clinical Genetics Resource - a comprehensive clinically annotated database and resource for genetic variants in ATP7A gene.

Computational and Structural Biotechnology Journal. Accepted (2020)


[156] Raxwal VK, Ghosh S, Singh S, Katiyar-Agarwal S, Goel S, Jagannath A, Kumar A, Scaria V, Agarwal M

Abiotic stress mediated modulation of chromatin landscape in Arabidopsis thaliana

Journal of Experimental Botany (2020), eraa286, https://doi.org/10.1093/jxb/eraa286


[155] Kumar M, Gaharwar U, Paul S, Poojary M, Pandhare K, Scaria V, Binukumar BK

WilsonGen a comprehensive clinically annotated genomic variant resource for Wilson’s Disease

Scientific Reports (2020) 10, : 9037


[154] Poojary M, Shantaraman A, Jolly B, Scaria V

Computational Protocol for Assembly and Analysis of SARS-nCoV-2 Genomes

Research Reports (2020) Accepted [COVID-19]


[153] Rophina M, Sharma D, Poojary M and Scaria V

circad: a comprehensive manually curated resource of circular RNA associated with diseases

Database (2020) Accepted [circAD Resource]


[152] 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 Sjogren’s syndrome reveals a distinct set of microbes associated with the disease

Oral Diseases (2019) Accepted


[151] 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

Molecular and Cellular Biochemistry (2020), https://doi.org/10.1007/s11010-020-03713-x


[150] 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 Feb;17(1):1-10. doi: 10.1089/zeb.2019.1790. Epub 2019 Nov 26.

2019

[149] GUaRDIAN Consortium

Genomics of rare genetic diseases—experiences from India

Human Genomics (2019) Accepted


[148] 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 Sep 6:144107. doi: 10.1016/j.gene.2019.144107


[147] 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 Jun;15(2):205-210. doi: 10.1007/s11302-019-09660-7. Epub 2019 May 31.


[146] Thottath J, Vellarikkal SK, Jayarajan R, Verma A, Manamel M, Singh A, Rajendran VR, Sivasubbu S and Scaria V

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

Neurol Genet 5:e302 (2019). doi:10.1212/NXG.0000000000000302


[145] Bandesh K, Jha P, Giri AK, Marwaha RK, Scaria V, Tandon N, Bharadwaj D

Normative range of blood biochemical parameters in urban Indian school-going adolescents

PLoS ONE 14(3): e0213255. https://doi.org/10.1371/journal.pone.0213255


[144] 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

Scientific Reports 9, 3432 (2019)


[143] Sivadas A, Scaria V

Population-scale genomics—Enabling precision public health

Advances in Genetics (Academic Press) (2019) https://doi.org/10.1016/bs.adgen.2018.09.001


[142] Sharma D, Sehgal S, Hariprakash J, Sivasubbu S, and Scaria V

Methods for Annotation and Validation of Circular RNAs from RNAseq Data

Methods Mol Biol. (2019) Accepted


[141] Mathew S, Sivadas A, Sehgal P, Kaushik K, Vellarikkal SK, Scaria V, and Sivasubbu S

Methods to Study Long Non-coding RNA Expression and Dynamics in Zebrafish using RNA Sequencing

Methods Mol Biol. (2019) Accepted

2018

[140] GBD 2017 Mortality Collaborators

Global, regional, and national age-sex-specific mortality and life expectancy, 1950–2017: a systematic analysis for the Global Burden of Disease Study 2017

The Lancet (2018) DOI: https://doi.org/10.1016/S0140-6736(18)31891-9


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

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

PLoS ONE 13 (9), e0204234


[138] 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,* and Sivasubbu S*

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

Database (2018) Vol. 2018: article ID bay080; doi:10.1093/database/bay080


[137] Yenamandra VK, Vellarikkal SK, Chowdhury MR, Jayarajan R, Verma A, Scaria V, Sivasubbu S, Basu Ray S, 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) Mar 27. doi: 10.2340/00015555-2929. [Epub ahead of print]


[136] Vellarikkal SK, Jayarajan R, Verma A, Ravi R, Senthilvel 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-1 in north Indian kindred

Clinical Genetics (2018) Accepted


[135] 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) https://doi.org/10.1016/j.gene.2018.03.062


[134] S Jalali, S Gandhi, V Scaria

Distinct and modular organisation of protein interacting sites in long non-coding RNAs

Frontiers in Molecular Biosciences 5, 27 (2018)


[133] Sivakumar S, Vimal S, Majeed SA, Kumar SS, Taju G, Madan N, Rajkumar T, Thamizhvanan S, Shamsudheen KV, Scaria V, Sivasubbu S, Hameed ASS

A new strain of white spot syndrome virus affecting Litopenaeus vannamei in Indian shrimp farms

J Fish Dis. (2018) ;1–18 DOI: 10.1111/jfd.12811


[132] Jain, A, Gandhi S, Koshy R, Scaria V*

Incidental and clinically actionable genetic variants in 1005 whole exomes and genomes from Qatar

Molecular Genetics and Genomics (2018) Accepted


[131] Sivadas A, Scaria V

Pharmacogenomic survey of Qatari populations using whole genome and exome sequences

The Pharmacogenomics Journal. (2018) Accepted


[130] Sabharwal A, Sharma D, Vellarikkal SK, Jayarajan R, Verma R, Senthivel V, Scaria V, Sivasubbu S

Organellar transcriptome sequencing reveals mitochondrial localization of nuclear encoded transcripts

Mitochondrion (2018) Accepted


[129] Mahajan R, Vellarikkal SK, Handa S, Verma A, Jayarajan R, Kumar A, De D, Kaur J, Panigrahi I, Vineeth VSI, 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

Journal of the European Academy of Dermatology and Venereology (2018) Accepted


[128] Babu A; Kamaraj M; Basu M; Mukherjee D; Kapoor S; Ranjan S; Swamy MM; Kaypee S; Scaria V; Kundu TK; Sachidanandan C.

Chemical and genetic rescue of an ep300 knockdown model for Rubinstein Taybi Syndrome in zebrafish

BBA - Molecular Basis of Disease (2018) Accepted


[127] 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) Accepted


[126] 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) Accepted


[125] Alinejad-Rokny H, Sadroddiny E, Scaria V

Machine learning and data mining techniques for medical complex data analysis

Neurocomputing (2018) 276:1 doi: 10.1016/j.neucom.2017.09.027

2017

[124] Ghosh S, Ranawat AS, Tolani P , Scaria V

MitoepigenomeKB a comprehensive resource for human mitochondrial epigenetic data

Mitochondrion (2017) Accepted


[123] Hariprakash JM, Vellarikkal SK, Keechilat P, Verma A, Jayarajan R, Dixit V, Ravi R, Senthivel V, Kumar A, Sehgal P, Aradhana, 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 (2017) Accepted


[122] Yenamandra V.K, Bhari N. Ray S.B, Sreenivas V., Dinda A.K, Scaria V, Sharma V.K, Sethuraman G

Diagnosis of Inherited Epidermolysis Bullosa in Resource-Limited Settings: Immunohistochemistry Revisited

Dermatology (2017) https://doi.org/10.1159/000478856


[121] 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


[120] Narayanan R, Karuthedath Vellarikkal S, Jayarajan R, Verma A, Dixit V, Scaria V and Sivasubbu S

Case Report: Application of whole exome sequencing for accurate diagnosis of rare syndromes of mineralocorticoid excess

F1000Research (2017) 5:1592 (doi: 10.12688/f1000research.8779.2)


[119] 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

F1000Research 2017, 5:2532 (doi: 10.12688/f1000research.9473.2)


[118] Jalali S, Singh A, Maiti S and Scaria V

Genome-wide computational analysis of potential long noncoding RNA mediated DNA:DNA:RNA triplexes in the Human genome

Journal of Translational Medicine (2017) Accepted


[117] Rawat A, Vellarikkal SK, 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

F1000Research (2017), 5:2667 (doi: 10.12688/f1000research.9472.2)


[116] Scaria V

Enabling Genomic Medicine in Qatar - from Genomes to Translational Genomics

Research Reports, 1(1) Aug 28, 2017


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

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

Scientific Reports (2017) Accepted


[114] Jithesh PV, Scaria V

From Genomes to Genomic Medicine- Enabling Personalised and Precision Medicine in the Middle East

Personalized Medicine (2017) Accepted


[113] Koshy R, Sivadas A, Scaria V.

Genetic epidemiology of Familial Mediterranean Fever through integrative analysis of whole genome and exome sequences from Middle East and North Africa

Clinical Genetics (2017) Accepted


[112] Koshy R, Ranawat A, Scaria V.

al mena - a comprehensive resource of human genetic variants integrating genomes and exomes from Arab, Middle Eastern and North African populations.

Journal of Human Genetics (2017) Accepted


[111] Balloy V, Koshy R, Perra L, Corvol H, Chignard M, Guillot L* and Scaria V*

Bronchial epithelial cells from Cystic Fibrosis patients express a specific long noncoding RNA signature upon Pseudomonas aeruginosa infection

Front. Cell. Infect. Microbiol. (2017) doi: 10.3389/fcimb.2017.00218


[110] 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) in press.


[109] Arora S, Jamal S, Gaba S, Hasija Y and Scaria V

Computational Modeling of Small Molecule Inhibitors of Mitochondrial Fusion

Current Bioinformatics (2017) Accepted DOI: 10.2174/1574893611666161103152934


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

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

Int J Rheum Dis (2017) Accepted


[107] Periwal V and Scaria V

Machine Learning Approaches Toward Building Predictive Models for Small Molecule Modulators of miRNA and Its Utility in Virtual Screening of Molecular Databases.

Methods Mol Biol. (2017)1517:155-168.

2005-2016

2016


[106] Jalali S, Gandhi S, Scaria V

Navigating the dynamic landscape of long noncoding RNA and protein-coding gene annotations in GENCODE

Human Genomics (2016)10 (1), 35


[105] Sivadas A, Sharma P, Scaria V

Landscape of warfarin and clopidogrel pharmacogenetic variants in Qatari population from whole exome datasets

Pharmacogenomics (2016) Accepted


[104] Asad Z, Pandey A, Babu A, Sun Y, Shevade K, Kapoor S, Ullah I, Ranjan S, Scaria V, Bajpai R, Sachidanandan C

Rescue of neural crest derived phenotypes in a zebrafish CHARGE model by sox10 downregulation

Hum. Mol. Genet. (2016) Accepted (doi: 10.1093/hmg/ddw198)


[103] Vellarikkal SK, 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

F1000Research 2016, 5:900


[102] Bhattacharjee J, Das B, Sharma D, Sahay P, Jain K, Mishra A, Iyer S, Nagpal P, Scaria V, Nagarajan P, Khanduri P, Mukhopadhyay A, Upadhyay P

Autologous NeoHep derived from chronic HBV patients’ blood monocytes by upregulation of cMET signalling

Stem Cell Transl Med (2016) Accepted


[101] Dey R, Soni K , Saravanan S, Balakrishnan P, Kumar V, Boobalan J, Solomon SS, Scaria V, Solomon S, Brahmachari SK, Pillai B

Anti-HIV microRNA expression in a novel Indian cohort

Scientific Reports (2016) Accepted


[100] Sivadas A, Salleh MZ, Teh LK, Scaria V*

Genetic epidemiology of pharmacogenetic variants in South East Asian Malays using whole genome sequences

The Pharmacogenomics Journal (2016) Accepted


[99] 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 Genet. 2016 Apr 15;12(4):e1005954


[98] Ahirwar R, Vellarikkal SK, Sett A, Sivasubbu S, Scaria V, Bora U, Borthakur BB, Kataki AC, Sharma JD, Nahar P

Aptamer-assisted detection of the altered expression of estrogen receptor alpha in human breast cancer

PLoS ONE (2016) Accepted


[97] Ghosh S, Sengupta S, Scaria V*

Hydroxymethyl cytosine marks in the human mitochondrial genome are dynamic in nature

Mitochondrion (2016) Accepted

First Genome-scale map of Hydroxymethyl cytosines in Human mitochondria


[96] 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) Accepted


[95] Bhartiya D, Scaria V*

Genomic variations in non-coding RNAs: Structure, Function and Regulation

Genomics (2016) Accepted


2015


[94] Ghosh S, Singh KK, Sengupta S, Scaria V*

Mitoepigenetics: the different shades of grey

Mitochondrion (2015) Accepted


[93] Gupta A, Sharma Y, Deo K , Vellarikkal S, Jayarajan R, Dixit V, Verma A, Scaria V* and Sivasubbu S*

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.

F1000Research (2015), 4:446


[92] Sandhya P, Joshi K , Scaria V*

Long noncoding RNAs could be potential key players in the pathophysiology of Sjögren’s syndrome

Int J Rheum Dis (2015) Accepted


[91] Sandhya P*, Danda D, Sharma D, Scaria V*

Does the buck stop with the bugs?:an overview of microbial dysbiosis in rheumatoid arthritis

Int J Rheum Dis (2015) Accepted


[90] Dhiman H, Kapoor S, Sivadas, A, Sivasubbu S*, Scaria V*

zflncRNApedia: a comprehensive online resource for zebrafish long non-coding RNAs

PLoS ONE (2015) Accepted


[89] 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) Accepted


[88] Jalali S, Kapoor S, Sivadas A, Bhartiya D, Scaria V*

Computational approaches towards understanding human long noncoding RNA biology

Bioinformatics (2015) Accepted


[87] 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, OSDD Consortium, Chauhan DS*, Sivasubbu S*, Scaria V*

Comparative Whole-Genome Analysis of Clinical Isolates Reveals Characteristic Architecture of Mycobacterium tuberculosis Pangenome

PLoS ONE (2015) Accepted


[86] 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

Human Mutation (2015) Accepted


[85] Periwal V, Scaria V*

Insights into structural variations and genome re-arrangements in prokaryotic genomes

Bioinformatics (2015) Jan 1;31(1):1-9. Epub 2014 Sep 4.


[84] Gupta A, Sharma YK, Vellarikkal SK, Jayarajan R, Dixit V , Verma A ,Sivasubbu S and Scaria V*

Whole-exome sequencing solves diagnostic dilemma in a rare case of sporadic acrokeratosis verruciformis

Journal of the European Academy of Dermatology and Venereology (2015) Accepted


[83] Scaria V

Joining the long shots: emerging evidence on the role of long noncoding RNAs in rheumatoid arthritis

Int J Rheum Dis (2015) Accepted


[82] Behera B, Das P, Maharana J, Paria P, Mandal S, Meena D, Sharma A, Jayarajan R, Dixit V, Verma A, Vellarikkal S, Scaria V, Sivasubbu S, Rao A and Mohapatra T

Draft Genome Sequence of the extremely halophilic Bacterium Halomonas salina sp. Strain CIFRI1 isolated from East Coast of India

Genome Announc. (2015) January/February 2015 3:e01321-14; doi:10.1128/genomeA.01321-14


[81] Ghosh S, Sati S, Sengupta S* and Scaria V*

Distinct patterns of epigenetic marks and transcription factor binding sites across promoters of sense-intronic long non-coding RNAs

J Genetics (2015) Accepted


2014


[80] Sahajpal R, Kandoi G, Dhiman H, Raj S, OSDD Consortium, Scaria V, Bhartiya D and Hasija Y

HGV&TB: A comprehensive online resource on Human genes and genetic variants associated with Tuberculosis

Database (2014) Accepted


[79] Gaba S, Jamal S, OSDD Consortium and Scaria V*

Cheminformatics models for inhibitors of Schistosoma mansoni Thioredoxin Glutathione Reductase

The Scientific World Journal (2014) Accepted


[78] Ghosh S, Sengupta S* and Scaria V*

Comparative analysis of Human mitochondrial methylomes show distinct patterns of epigenetic regulation in mitochondria

Mitochondrion (2014) Accepted

First Genome-scale map of methyl cytosines in Human mitochondria


[77] Vij S, Purushothaman K, Gopikrishna G, lau D, Saju J, Vellarikkal SK, Kumar VK, Basheer VS, Gopalakrishnan A, Hossain M, Sivasubbu S, Scaria V, Jena JK, Ponniah AG and Orbán L*

Barcoding of Asian seabass across its geographic range provides evidence for its bifurcation into two distinct species

Front. Mar. Sci. (2014) Accepted


[76] Haque S, Kaushik K, Leonard VE, Kapoor S, Sivadas A, Joshi A, Scaria V*, Sivasubbu S*

Short stories on zebrafish long noncoding RNAs

Zebrafish (2014) Accepted


[75] Vellarikkal SK, Patowary A, Singh M, Kumari R, Faruq M, Master DC, Sivasubbu S*and 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) Accepted


[74] Jamal S, OSDD Consortium, Scaria V

Data-mining of potential antitubercular activities from molecular ingredients of Traditional Chinese Medicines

PeerJ (2014) Accepted


[73] Giri AK, Khan NM, Grover S, Kaur I, Basu A, Tandon N, Scaria V, Consortium IGI, INDICO*, Kukreti R, Brahmachari SK, Bharadwaj D

Genetic epidemiology of pharmacogenetic variations in CYP2C9, CYP4F2 and VKORC1 genes associated with Warfarin dosage in Indian population

Pharmacogenomics (2014) Accepted


[72] Rajpathak SN, Vellarikkal SK,Patowary A, Scaria V*, Sivasubbu S* and 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) Accepted


[71] Hasija Y, Khan JA, Scaria V*

Pharmacogenomics for Precision Medicine in the era of collaborative co-creation and crowdsourcing

Current Genetic Medicine Reports (2014) Accepted


[70] Scaria V*

Personal genomes, participatory genomics and the anonymity-privacy conundrum

J Genetics (2014) Accepted


[69] Singh M, Bhartiya D,Maini J,Sharma M,Singh AR, Subburaj K, Rana R, Sabharwal A, Nanda S, Aravindhakshan R, Mittal A, Kapoor S, Sehgal P, Asad Z, Kaushik K, Vellarikkal SK, Jagga D, Muthulakshmi. M1, 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* and Sivasubbu S*

The Zebrafish GenomeWiki: A crowdsourcing approach to connect the long tail for zebrafish gene annotation

Database (2014) Accepted


[68] Tiwari P, Joshi K, Rehman R, Bhardwaj V, Shamsudheen KV, Sivasubbu S*, and Scaria V*

Draft genome sequence of urease producing Sporosarcina pasteurii with potential application in bio-cement production

Genome Announc. (2014) Jan 30;2(1). pii: e01256-13..


[67] Giri AK, Khan NM, Narayanan D, INDICO, Basu A, Tandon N, Scaria V*, Bharadwaj D*

Pharmacogenetic landscape of Clopidogrel in North Indians suggest distinct inter-population differences in allele frequencies

Pharmacogenomics (2014) Accepted


[66]Joshi KR, Dhiman H, Scaria V*

tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis

Database (2014) 2014: bat083.


[65] Jamal S, Arora S , Scaria V*

Computational analysis and predictive cheminformatics modeling of small molecule inhibitors of epigenetic modifiers

PLoS ONE (2014) Accepted


[64] Bhartiya D, Jalali S, Ghosh S, Scaria V*

Distinct patterns of genetic variations in potentially functional elements in long noncoding RNAs

Human Mutation (2014) Feb;35(2):192-201


2013


[63] 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).


[62] Kaushik K, Leonard VE, Shamsudheen KV, Lalwani MK, Jalali S, Patowary A, Joshi A, Scaria V*and Sivasubbu S*

Dynamic Expression of Long Non-coding RNAs (lncRNAs) in Adult Zebrafish

PLoS ONE (2013) Dec 31;8(12):e83616.


[61] 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).


[60] Vellarikkal SK, 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)


[59] Jamal S, OSDD Consortium, Scaria V*

Cheminformatic models based on machine learning for pyruvate kinase inhibitors of Leishmania mexicana

BMC Bioinformatics (2013) 14 (1), 329.


[58] Sivasubbu S, Sachidanandan C, Scaria V

Time for the zebrafish ENCODE

Journal of Genetics (2013) Dec;92(3):695-701.


[57] Salleh MZ*, Teh LK, Lee LS, Ismet RI, Patowary A, Joshi K, Pasha A, Ahmed AZ, Janor MH, Hamzah AS, Adam I, Yusoff K, Hoh BP, Hatta FM, Ismail MI, Scaria V*, Sivasubbu S*

Systematic Pharmacogenomics analysis of a Malay whole genome : Proof of concept for Personalised Medicine.

PLoS ONE (2013) Aug 23;8(8):e71554.


[56] Vellarikkal SK, Patowary A, Singh M, Periwal V, Singh A, Singh P, Garg P, Katoch VM, Katoch K, Jangir P, Sharma R, OSDD Consortium, Chauhan DS, Scaria V, and Sivasubbu S

Draft genome sequence of a multi-drug resistant Mycobacterium tuberculosis East African Indian (EAI) clinical isolate OSDD271

Genome Announcements (2013) Aug 1;1(4). pii: e00541-13.


[55] Pore SK, Choudhary A, Rathore B, Ganguly A, Sujitha P , Kumar CG, Agawane SB, Kumar JM ,Scaria V, Pillai B, Banerjee R.

Hsp90-targeted miRNA-liposomal formulation for systemic antitumor effect

Biomaterials (2013) Sep;34(28):6804-17


[54] Bhartiya D,Pal K, Ghosh S, Kapoor S, Jalali S, Panwar B, Jain S, Sati S, Sengupta S, Sachidanandan C, Raghava GPS, Sivasubbu S and Scaria V*

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs

Database (2013) Jul 11;2013:bat034.


[53] Patowary A, Purkanti R, Singh M, Chauhan R,Singh AR, Swarnkar M, Singh N, Pandey V, Torroja C, Clark MD, Kocher J, Clark KJ, Stemple DL, Klee EW, Ekker SC*, Scaria V*, Sivasubbu S*

A sequence-based variation map of zebrafish

Zebrafish (2013) March 2013, 10(1): 15-20.


[52] Mole S, Jalali S, Scaria V, Bhardwaj A

MitoLSDB: A Comprehensive Resource to Study Genotype to Phenotype Correlations in Human Mitochondrial DNA Variation

PLoS ONE (2013) Apr 9;8(4):e60066.


[51] Jamal S, Periwal V, OSDD Consortium and Scaria V

Predictive cheminformatics analysis of anti-malarial molecules inhibiting apicoplast formation

BMC Bioinformatics (2013) 14:55


[50] Jalali S, Bhartiya D, Lalwani MK, Sivasubbu S*, Scaria V*

Systematic transcriptome wide analysis of lncRNA-miRNA interactions.

PLoS One (2013) 8(2): e53823.


[Book Chapter]Pasha A and Scaria V

Pharmacogenomics in the era of personal genomics: a quick guide to online resources and tools

in Omics for Personalised Medicine [Edited by Barh D, Dhawan D, and Ganguly NK] Springer 2013


2012


[49] Scaria V*, Pasha A

Long noncoding RNAs in infection biology

Front. Genet.3:308 (2012)


[48] Tabassum R, Chauhan G, Dwivedi OP,Mahajan A, Jaiswal A, Kaur I, Bandesh K,Singh T, Mathai BJ, Pandey Y,Chidambaram M, Sharma A, Chavali S,Sengupta S, Ramakrishnan L, Venkatesh P,Aggarwal SK, Ghosh S, Prabhakaran D,Srinath RK, Saxena M, Banerjee M,Mathur S, Bhansali A, Shah VN, Madhu SV,Marwaha RK, Basu A, Scaria V, McCarthy MI,DIAGRAM, INDICO, Venkatesan , Mohan V,Tandon N, Bharadwaj D

Genome-wide Association Study for Type 2 Diabetes in Indians Identifies a New Susceptibility Locus at 2q21

Diabetes (2012) published ahead of print December 3,


[47] Lalwani MK, Sharma M, Singh RA, 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 7(12): e52588.


[46] Jamal S, Periwal V, OSDD Consortium, Scaria V*

Computational analysis and predictive modeling of small molecule modulators of microRNA

Journal of Cheminformatics (2012), 4:16


[45] Sati S, Ghosh S; Jain V, Scaria V*, Sengupta S*

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

Nucl. Acids Res. (2012) 40 (20):10018-10031.


[44] Jalali S, Jayaraj GG, Scaria V

Integrative transcriptome analysis suggest processing of a subset of long non-coding RNAs to small RNAs

Biology Direct 2012, 7:25


[43] Bargaje R, Alam P, 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.

Nucl. Acids Res. (2012) 40 (18):8965-8978.


[42] Bhartiya D, Talwar J, Hasija Y, Scaria V

Systematic curation and analysis of genomic variations and their potential functional consequences in snoRNA loci

Human Mutation (2012), 33: E2367–E2374.


[41] 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.


[40] 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., 33: 1133–1140.


[39] Periwal V, Kishtapuram S, Open Source Drug Discovery Consortium and Scaria V

Computational models for in-vitro anti-tubercular activity of molecules based on high-throughput chemical biology screening datasets

BMC Pharmacology (2012), 12:1


[38] Sati S, Tanwar VS, Kumar KA, Patowary A, Jain V, Ghosh S, Ahmad S, Singh M, S Reddy U, 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 7(2): e31621.


[37] Vashisht R, Mondal AK, Jain A, Shah A, Vishnoi P, Priyadarshini P, Bhattacharyya K, Rohira H, Bhat AG, Passi A, Mukherjee K, Choudhary KS, Kumar V, Arora A, Munusamy P, Subramanian A, Venkatachalam A, S G, Raj S, Chitra V, Verma K, Zaheer S, J B, Gurusamy M, Razeeth M, Raja I, Thandapani M, Mevada V, Soni R, Rana S, Ramanna GM, Raghavan S, Subramanya SN, Kholia T, Patel R, Bhavnani V, Chiranjeevi L, Sengupta S, Singh PK, Atray N, Gandhi S, Avasthi TS, Nisthar S, Anurag M, Sharma P, Hasija Y, Dash D, Sharma A, Scaria V, Thomas Z; OSDD Consortium, Chandra N, Brahmachari SK, Bhardwaj A.

Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis.

PLoS One. 2012;7(7):e39808. Epub 2012 Jul 11.


[36] Suryawanshi H, Lalwani MK, Ramsamy Soundhar,Rana R,Scaria V, Sivasubbu S, Maiti S

Antagonism of microRNA function in zebrafish embryos using Locked Nucleic Acid Enzymes(LNAzymes)

ChemBioChem, (2012) 13: 584–589.


[35] Jayaraj GG, Pandey S, Scaria V*, Maiti S*

Potential G-quadruplex forming sequences in the Human non-coding transcriptome

RNA Biology 2012 9:1


[34] Kandoi G, Nanda, A, Scaria V*, Sivasubbu S*

A case of pharmacogenomics in management of cardiac arrhythmias

Indian Pacing and Electrophysiology J (2012) 2012;12(2):54-64


[33] Patowary A, Chauhan RK, Singh M, Shamsudheen KV, Periwal V, Kushwaha KP, Sapkal GN, Bondre VP, Gore MM, Sivasubbu S and Scaria V

De novo identification of viral pathogens from cell culture hologenomes

BMC Research Notes 2012, 5:11


2011


[32] Indian Diabetes Consortium^

INDICO: the development of a resource for epigenomic study of Indians undergoing socioeconomic transition

HUGO Journal (2011) Accepted


[31] Periwal V, Jinuraj KR, OSDD Consortium, Jaleel UC* and Scaria V*

Predictive models for anti-tubercular molecules using machine learning on high-throughput biological screening datasets

BMC Research Notes 2011 18;4:504.


[30] Karl J Clark, Darius Balciunas, Hans-Martin Pogoda, Yonghe Ding, Stephanie E Westcot, Victoria M Bedell, Tammy M Greenwood, Mark D Urban, Kimberly J Skuster, Andrew M Petzold, Jun Ni, Aubrey L Nielsen, Ashok Patowary, Vinod Scaria, Sridhar Sivasubbu, Xiaolei Xu, Matthias Hammerschmidt & Stephen C Ekker

In vivo protein trapping produces a functional expression codex of the vertebrate proteome

Nature Methods 2011 8(6):506-15. Featured Article


[29] Bhardwaj A, Scaria V, Raghava GPS, Lynn AM, Chandra N, Banerjee S, Raghunandanan MV, Pandey V,

Taneja B, Yadav J, Dash D, Bhattacharya J, Misra A, Kumar A, Ramachandran S, Thomas Z, Brahmachari SK.

Open source drug discoverye A new paradigm of collaborative research in tuberculosis drug development

Tuberculosis 2011 91(5):479-86.


[28] Bhartiya D, Laddha, SV, Mukhopadhyay A, Scaria, V*

miRvar: A Comprehensive Database and Systematic Analysis of Genomic Variations in microRNAs

Human Mutation 2011;32(6):E2226-45


[27] Bhardwaj A*, Scaria V*, Patra D, Open Source Drug Discovery Consortium

Open Source Drug Discovery : A Global Collaborative Drug Discovery Model for Tuberciulosis

Science and Culture (Jan-Feb 2011)


[26] 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


[Book Chapter]

Bhardwaj A, Scaria V, Thomas Z, Adayikkoth S, Open Source Drug Discovery (OSDD) Consortium & Brahmachari SK

Collaborative Tools to Accelerate Neglected Disease Research: the Open Source Drug Discovery Model

in Collaborative Computational Technologies for Biomedical Research (2011)


2010


[25] Kaur H, Scaria V, Maiti S

Locked onto the Target’: Increasing the efficiency of antigomirzymes using LNA – modifications

Biochemistry (2010) Accepted


[24] Suryawanshi H, Scaria V , Maiti S

Modulation of microRNA Function by Synthetic Ribozymes

Molecular Biosystems (2010) Accepted


[23] 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*, and Sivasubbu S*

FishMap Zv8 Update—A Genomic Regulatory Map of Zebrafish

Zebrafish (2010) Accepted


[22] Bargaje R, Hariharan M, Scaria V, Pillai B

Consensus miRNA expression profiles derived from interplatform normalization of microarray data.

RNA. 2010 Jan;16(1):16-25.


2009


[21] HUGO PASNPI Consortium#

Mapping Human Genetic History in Asia

Science 2009 (Accepted)


[20] Roshan R, Ghosh T, Scaria V, Pillai B.

MicroRNAs: novel therapeutic targets in neurodegenerative diseases.

Drug Discov Today. 2009 Oct 9.


[19] Kumar S, Ansari FA, Scaria V*

Prediction of viral microRNA precursors based on human microRNA precursor sequence and structural features.

Virology Journal 2009, 6:129


[18] Bhardwaj A, Bhartiya D, Kumar N, Open Source Drug Discovery Consortium, Scaria V*

TBrowse: an Integrative Genomics Map of Mycobacterium tuberculosis.

Tuberculosis 2009 Aug 13 [Epub ahead of print]


[17] Chhabra R, Adlakha YK, Hariharan M, Scaria V, Saini N

Upregulation of miR-23a~27a~24-2 Cluster Induces Caspase-Dependent and -Independent Apoptosis in Human Embryonic Kidney Cells.

PLoS ONE 2009 4(6): e5848


[16] Hariharan M, Scaria V, Brahmachari SK .

dbSMR: A Novel Resource of Genome-wide SNPs affecting MicroRNA Mediated Regulation

BMC Bioinformatics 2009 Apr 16;10:108.


[15] Faruq M, Scaria V, Singh I, Tyagi S, Srivastava AK, Mukerji M

SCA-LSVD: A repeat oriented locus specific variation database for genotype to phenotype correlations in Spinocerebellar Ataxias

Human Mutation 2009 Jul;30(7):1037-42.


[14] Jadhav VM, Scaria V, Maiti S Featured Article

Antagomirzymes: Oligonucleotide enzymes specifically silence microRNA function

Angewandte Chemie 2009 48(14):2557-60.


2008


[13] Ahluwalia J, Khan S, Soni K, Rawat P, Gupta A, Hariharan M, Scaria V, Lalwani M, Pillai B, Mitra D, Brahmachari S .

Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication

Retrovirology 2008, 5:117

[Also see: HGM2008 Poster Abstract]


[12] Ghosh T, Soni K, Scaria V, Halimani M, Bhattacharjee C, Pillai B

MicroRNA-mediated up-regulation of an alternatively polyadenylated variant of the mouse cytoplasmic {beta}-actin gene.

Nucleic Acids Res. 2008 Oct 3;


[11] Meli R, Prasad A, Patowary A, Lalwani MK, Maini MK, Sharma M,

Singh AR, Kumar G, Jadhav V, Scaria V*, Sivasubbu S.

FishMap: A community resource for Zebrafish genomics.

Zebrafish June 1, 2008, 5(2): 125-130 Cover Article


[10] Arora A , Dutkiewicz M, Scaria V , Hariharan M, Maiti S , Kurreck J.

Inhibition of translation in living eukaryotic cells by an RNA G-quadruplex motif

RNA (2008), 14:1–7. Featured on Cover


[9] Indian Genome Variation Consortium*

Genetic Landscape of the People of India: a Canvas for Disease Gene Exploration

J Genetics 2008 (accepted) (*as co-author of the consortia) Cover Article


2007


[8] Scaria V*, Jadhav V.

microRNAs in viral oncogenesis.

Retrovirology. 2007 Nov 24;4(1):82


[7] Scaria V, Hariharan M, Pillai B, Maiti S, Brahmachari SK.

Host-virus genome interactions: macro roles for microRNAs.

Cell Microbiol. 2007 Nov 6;9(12):2784-2794.


[6] Scaria V, Hariharan M, Pillai B, Maiti S, Brahmachari SK.

microRNA: an Emerging Therapeutic

ChemMedChem 2007 (in press)


[5] The NMITLI-BioSuite Team*

BioSuite: A comprehensive bioinformatics software package (A unique industry–academia collaboration)

Current Science. 2007 Jan 92(1): 29-38

(*as co-author of the consortia)


2006


[4] Scaria V, Hariharan M, Maiti S, Pillai B, Brahmachari SK.

Host-Virus interaction: A new role for microRNAs

Retrovirology 2006 3:68 (11 October 2006)


[3] Harish N, Gupta R, Agarwal P, Scaria V, Pillai B.

DyNAVacS: an integrative tool for optimized DNA vaccine design.

Nucleic Acids Res. 2006 Jul 1;34:W264-6.

(Co-corresponding author)


[2] Scaria V, Hariharan M, Arora A, Maiti S.

Quadfinder: server for identification and analysis of quadruplex-forming motifs in nucleotide sequences.

Nucleic Acids Res. 2006 Jul 1;34:W683-5.


2005


[1] Hariharan M, Scaria V, Pillai B, Brahmachari SK

Targets for human encoded microRNAs in HIV genes.

Biochem Biophys Res Commun. 2005 Dec 2;337(4):1214-8.

(Co-first author)


From the Calicut Medical College (2000-2004)


2004


[8] Ramachandran PV, Scaria V.

Open Access Publishing in the Developing World: making a difference.

J.Orthopaedics 2004;1(1)e1


[7] Scaria V.

Cyber-pharmacies and ethical concerns over marketing drugs online*.

Eubios J Asian Int Bioethics 14 (2004), 61-63


[6] Scaria V.

Whisking Research into Medical Curriculum: The need to integrate research in undergraduate medical education to meet the future challenges.

Calicut Medical Journal 2004;2(1):e1


2003


[5] Scaria V.

Peer Review of Scholarly Communication in Health: Perspectives in the Internet Age.

Online J Health Allied Scs.2003;1:2


[4] Scaria V.

Unsolicited Commercial E-Mail,Spam and Terrorism; An Ethical Discussion*.

Eubios J Asian Int Bioethics. 2003;13:111-112


[3] Scaria V.

Cyber-pharmacies and emerging concerns on marketing drugs Online.

Online J Health Allied Scs. 2003;2:1


[2] Scaria V.

Buying Sildenafil Citrate (Viagra®) Online: Are prospective buyers informed of Contraindications? *.

Calicut Medical Journal 2003;1(1)e4


[1] Scaria V.

A discussion on the perspectives of Suicide related Information on the Internet.

Eubios J Asian Int Bioethics 13 (2003), 175-176