Publications

From the CSIR Institute of Genomics and Integrative Biology (2004-present)

2017

[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

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)

(Publications by Funding Agency)
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