Publications by Funding Agency


BSC0123 (GENCODE-C)

[11] Bhartiya D, Scaria V*
Genomic variations in non-coding RNAs: Structure, Function and Regulation
Genomics (2016) Accepted

[10] 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

[9] 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

[8] Jalali S, Kapoor S, Sivadas A, Bhartiya D, Scaria V
Computational approaches towards understanding human long noncoding RNA biology
Bioinformatics (2015) Accepted

[7] Scaria V 
Joining the long shots: emerging evidence on the role of long noncoding RNAs in rheumatoid arthritis
Int J Rheum Dis 
(2015) Accepted

[6] 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

[5] 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

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

[3] Kaushik K, Leonard VE, Shamsudheen KV, Lalwani MK, Jalali S, Patowary A, Joshi A, Scaria V*and Sivasubbu S*
PLoS ONE (2013) Dec 31;8(12):e83616. 

[2] Sivasubbu S, Sachidanandan C, Scaria V
Journal of Genetics (2013) Dec;92(3):695-701.

[1] 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*













































BSC0122 (CARDIOMED)

[17] Ghosh S, Sengupta S, Scaria V
Hydroxymethyl cytosine marks in the human mitochondrial genome are dynamic in nature 
Mitochondrion (2016) Accepted

[16] 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

[15] Ghosh S, Singh KK, Sengupta S, Scaria V*
Mitoepigenetics: the different shades of grey
Mitochondrion (2015) Accepted

[14] 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

[13] 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

[12] 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

[11] 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

[10] Ghosh S, Sengupta S* and Scaria V*
Comparative analysis of Human mitochondrial methylomes show distinct patterns of epigenetic regulation in mitochondria
Mitochondrion (2014) Accepted

[9] 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

[8] 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  

[7] 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

[6] Scaria V*
Personal genomes, participatory genomics and the anonymity-privacy conundrum
J Genetics (2014) Accepted

[5] 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

[4] 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 

[3] 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  

[2] Jamal S, Arora S , Scaria V*
Computational analysis and predictive cheminformatics modeling of small molecule inhibitors of epigenetic modifiers 
PLoS ONE (2014) Accepted

[1] 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.


OLP1105 (EMPOWER)

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

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.

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..

Patowary A, Chauhan RK, Singh M, Shamsudheen KV, Periwal V, Kushwaha KP, Sapkal GN, Bondre VP, Gore MM, Sivasubbu S and Scaria V
BMC Research Notes 2012, 5:11 

HCP001 (OPEN SOURCE DRUG DISCOVERY)

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

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

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

Jamal S, OSDD Consortium, Scaria V
Data-mining of potential antitubercular activities from molecular ingredients of Traditional Chinese Medicines 
PeerJ (2014) Accepted

Joshi KR, Dhiman H, Scaria V*
Database (2014) 2014: bat083.

Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S, Scaria V.
Genome Announc. 2013 Nov 21;1(6). 


Vellarikkal SK, Singh AV, Singh PK, Garg P, Katoch VM, Katoch K; Open Source Drug Discovery Consortium, Chauhan DS, Sivasubbu S, Scaria V.
Genome Announc. 2013 Nov 21;1(6). 

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.
Genome Announc. 2013 Nov 7;1(6)

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

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

BMC Bioinformatics (2013) 14:55

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

Front. Genet.3:308 (2012) 

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.

BMC Pharmacology (2012), 12:1