Aditya CV

ADITYA JAIN

Project Assistant at IISER Mohali
Indore Area, India
Biotechnology
Current
  1. ADITYA JAIN
Previous
  1. IISER Mohali, 
  2. Eminent Biosciences, 
  3. Aditya Bioinformatics Solutions
Education
  1. School of Life Science, Manipal university
Websites
  1. www.adityabioinfo.com


  • Project Assistant

    IISER Mohali
     –  (2 years 1 month)

  • Trainee under BIITP

    Eminent Biosciences
     –  (7 months)Indore Area, India
    Comparative analysis of primary tumour and matched metastases in cancer patients: Evaluation of concordance between genomic and transcriptional profiles

  • Executive Director

    Aditya Bioinformatics Solutions
     –  (1 year)
    We are not a company or any organization, There is no registration or fees involved. We believe in sharing knowledge. Students, Research scholars, trannies can contact us with there Bioinformatic problems we will try to solve the problems that also without any registration or fees. Just mail or call us with your problem and we will be there to help you.

  • Aditya jain

    EMINENT
     –  (2 years 3 months)
    ADITYA INDORE BIOINFORMATIC

  • FASHION PLAZA

    FASHION PLAZA
     –  (1 year 11 months)
    Fashion Plazaa

    -- a new trendy and funky store

  • Aditya jain

    EMINENTBIO SCIENCE
     –  (1 month)
    ADITYA JAIN INDORE BIOINFORMATIC

Education

  • School of Life Science, Manipal university

    Master of Science (MSc), Bioinformatics
     – 
    Masters in Bioinformatics
    Activities and Societies: member of college cricket team

  • MANIPAL LIFE SCIENCE CENTRE

    Master of Science (MSc), Bioinformatics
     – 
    MSc. Bioinformatics
    Activities and Societies: Swimming, Long jump, Relay race

  • Bioinformatics Softvision College

    Bachelor of Science (BSc), Bioinformatics
     – 
    BSc. Bioinformatics
    Activities and Societies: Bug hunter, Mad adds, Skit

  • EMERALD HEIGHTS INTERNATIONAL SCHOOL

    HIGH SCHOOL, Biology, General
     – 
    Biology
    Activities and Societies: Gym, Tennis, Swimming

Volunteer Experience & Causes

  • Certificate of volunteered towards collecting Fund for people affected by Tsunami

    Emerald Heights International school
     –  (11 months)

Skills

  • Bioinformatics
  • SQL
  • Genomics
  • C
  • C++
  • Biotechnology
  • Lifesciences
  • PCR
  • Operating Systems
  • Genetics
  • R
  • Drug Discovery
  • Validation
  • HPLC
  • Western Blotting
How's this translation?
  • Great
  • •
  • Has errors

Certifications

Courses

  • EMERALD HEIGHTS INTERNATIONAL SCHOOL

    • science

  • School of Life Science, Manipal university

    • BIOINFORMATICS

Honors & Awards

  • junior scientist

    softvision college
    January 2011

Languages

  • English

Projects

  • An integrated Repository of Computational Prediction of Deleterious SNPs Involved in Pathway of Bacterial Invasion of Epithelial Cells (BIoEC) in Homo sapiens

     – 
    polyBIoECP is a directory of all the synonymous (sSNP) and non synonymous (nsSNP) polymorphisms collected using SCAN database which are associated with various genes involved in bacterial invasion of epithelial cells pathway. Â It is an effort to evaluate the phenotypic effect of all known nsSNPs of the genes involved in BIoEC pathway and to enable researchers an easy access. To further validate, this database was developed with an updated list of all validated nsSNPs from dbSNP (NCBI) and their effect on the structure and functions of the proteins along with their genomic elements such as miRNA, CNV and CpG islands. BIoECP also has a comparative analysis of native and mutant protein (using MODELLER) of the respective polymorphism validated using Ramachandran Plot.
    Team members:

  • 1-CMDb: Database for variations in human one carbon metabolism pathway

     – 
    2.1. Aim:
    The aim of the present study was to find out the different levels of variations present in human one carbon folate metabolism pathway.
    2.2. Objectives:
    To find out the variations in one carbon metabolism pathway of human genome.
    To predict the disease associated CNV and SNPs in the one metabolic pathway.
    To develop a database for identified variations in human one carbon metabolic pathway.
    Team members:

  • Computational Analysis and Prediction of Deleterious SNPs Involved in Pathway of Bacterial Invasion of Epithelial Cells (BIoEC) in Homo sapiens

     – 
    Prevalence of complex resistance mechanism in many pathogenic bacteria helps them to circumvent the host defence mechanism and use epithelium as a replicative bridgehead. Single nucleotide polymorphisms in the genes involved in Bacterial Invasion of Epithelial Cells (BIoEC) results in either defective protein synthesis or reduced protein function thus favoring bacterial invasion and pervasiveness. In an effort to evaluate the phenotypic effect of all known nsSNPs of the genes involved in BIoEC pathway and to enable researchers easy access to further validate, we developed a database with an updated list of all validated nsSNPs from dbSNP (NCBI) and their effect on the structure and functions of the proteins along with their genomic elements.
    Team members:

  • A comparative study of available software for high accuracy homology modeling- from online server available

     – 
    With increase in knowledge of protein sequences it is necessary that we should know the function of the protein and to know the function we should have knowledge of its structure. We still do not know how protein folding takes place in nature, but with known similar protein structures we will be able to determine structure of protein through homology modelinga. Today there are many online automated servers available for homology modeling. But the question arises which tool should be best suited for an unknown protein? To solve this question we have examined the homology-built models of different proteins, variation in sequence identity across these proteins ranges from 30% to 90 % identity. All of the protein structures such as we have taken are modeled using online server through an automated mode of homology modeling. All the structures were evaluated using Procheck. On obtaining higher identity matches Swiss-model and 3D Jigsaw gave best results amongst the four online servers by comparing the energy parameter (phi) and (psi) angles and by seeing the residues falling in region of Ramachandran plot we come to a conclusion that. At lower identity matches Swiss-model and Cphmodels server gave best results. On comparing percentage of identities, from lower to higher, best results are obtained from Swiss-model. From this comparative study we can conclude that, out of the four online servers Swiss-model, 3D Jigsaw, Geno3d, Cphmodel server, Swiss model can be considered the best homology modeling online server.
    Team members:

  • molecular modelling

     – 
    Molecular modeling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, drug design, computational biology and materials science for studying molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling techniques is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (the Molecular mechanics approach), or explicitly modeling electrons of each atom (the quantum chemistry approach).
    Team members:

Publications

  • 1-CMDb: A Curated Database of Genomic Variations of the One-Carbon Metabolism Pathway

    Public Health Genome
    May 2017
    The one-carbon metabolism pathway is vital in maintaining tissue homeostasis by driving the critical reactions of folate and methionine cycles. A myriad of genetic and epigenetic events mark the rate of reactions in a tissue-specific manner. Integration of these to predict and provide personalized health management requires robust computational tools that can process multiomics data. The DNA sequences that may determine the chain of biological events and the endpoint reactions within one-carbon metabolism genes remain to be comprehensively recorded. Hence, we designed the one-carbon metabolism database (1-CMDb) as a platform to interrogate its association with a host of human disorders.
    Authors:

  • Categorical complexities of Plasmodium falciparum malaria in individuals is associated with genetic variations in ADORA2A and GRK5 genes.

    Elsevier, Infection, Genetics and Evolution
    August 2015
    In the erythrocytes, malaria parasite entry and infection is mediated through complex membrane sorting and signaling processes. We investigated the effects of single-locus and multilocus interactions to test the hypothesis that the members of the GPCR family genes, adenosine A2a receptor (ADORA2A) and G-protein coupled receptor kinase5 (GRK5), may contribute to the pathogenesis of malaria caused by Plasmodium falciparum (Pf) independently or through complex interactions. In a case-control study of adults, individuals affected by Pf malaria (complicated n=168; uncomplicated n=282) and healthy controls (n=450) were tested for their association to four known SNPs in GRK5 (rs2230345, rs2275036, rs4752307 and rs11198918) and two in ADORA2A (rs9624472 and rs5751876) genes with malaria susceptibility, using techniques of polymerase chain reaction-restriction fragment length polymorphisms and direct DNA sequencing. Single-locus analysis showed significant association of 2 SNPs; rs5751876 (OR=3.2(2.0-5.2); p=0.0006) of ADORA2A and rs2230345 (OR=0.3(0.2-0.5); p=0.0006) of GRK5 with malaria. . The study provides evidence for the role of ADORA2A and GRK5 that might influence the etiology of malaria infection.
    Authors:

  • Genetic association of KCNJ10 rs1130183 with seizure susceptibility and computational analysis of deleterious non-synonymous SNPs of KCNJ10 gene.

    GENE
    December 2013
    Establishing genetic basis of Idiopathic generalized epilepsies (IGE) is challenging because of their complex inheritance pattern and genetic heterogeneity. Kir4.1 inwardly rectifying channel (KCNJ10) is one of the independent genes reported to be associated with seizure susceptibility. In the current study we have performed a comprehensive in silico analysis of genetic variants in KCNJ10gene at functional and structural level along with a case-control analysis for the association ofrs1130183 (R271C) polymorphism in Indian patients with IGE. Age and sex matched 108epileptic patients and normal healthy controls were examined. Genotyping of KCNJ10rs1130183variation was performed using PCR-RFLP method. The risk association was determined by using odds ratio and 95% confidence interval. Functional effects of non-synonymous SNPs (nsSNPs) in KCNJ10 gene were analyzed using SIFT PolyPhen-2, I-Mutant 2.0, PANTHER and FASTSNP. Subsequently, homology modeling of protein three dimensional (3D) structures was performed using Modeller tool (9.10v) and compared the native protein with mutant for assessment of structure and stability. SIFT, PolyPhen-2, I-Mutant 2.0 and PANTHER collectively showed rs1130183, rs1130182 and rs137853073 SNPs inKCNJ10 gene affect protein structure and function. There was a considerable variation in the Root Mean Square Deviation (RMSD) value between the native and mutant structure (1.17Ǻ). Association analysis indicate KCNJ10rs1130183 did not contribute to risk of seizure susceptibility in Indian patients with IGE (OR- 0.38; 95%CI, 0.07-2.05) and T allele frequency (0.02%) was in concordance with dbSNP reports. This study identifies potential SNPs that may contribute to seizure susceptibility and further studies with the selected SNPs in larger number of samples and their functional analysis is required for understanding the variants of KCNJ10with seizure susceptibility.
    Authors:

  • Molecular modeling of Acetyl-CoA carboxylase (ACC) from Jatropha curcas and virtual screening for identification of inhibitors

    Journal of Pharmacy Research
    September 2013
    Aim : Acetyl-CoA carboxylase (ACC) is a biotin-dependent enzyme which plays a key role in fatty acid biosynthesis via production of melonyl-CoA as an essential substrate. It is involved in homeostasis of fatty acids inside the system using both up and down regulating mechanisms. Apart from this In silico analysis of its catalytic site and regulatory sites make it a potential target for herbicidal and insecticidal drug targeting. Currently the 3D structure of Acetyl-CoA carboxylase (ACC) from Jatropha curcas has not been solved in Protein Data Bank (PDB). Hence the aim of the present study is to build the 3D structure of Acetyl-CoA carboxylase (ACC) from J. curcas also to perform a virtual screening for the identification of the effective inhibitors using molecular docking studies.
    Methods: Homology modeling has been used to determine the 3D structure of Acetyl-CoA carboxylase (ACC) from J. curcas. Structure validation and molecular docking studies has been carried out using Procheck and Molegro Virtual Docker respectively.
    Results: Ramachandran Plot confirmed quality of modeled structures along with main chain and side chain parameters. Out of 309 residues in SPDBV model, 244 were in core region 19 residues were in additional allowed region, 2 residues were in generous allowed region and no residues were in disallowed region.
    Conclusion: Energy minimization for SPDBV model thermodynamically proved accepted structure with energy of −12,063.024 kJ/mol. The model further can be subjected to pharmacodynamic and pharmacokinetic studies. Molecular docking studies identified few established herbicides which could be promising inhibitors of Acetyl-CoA carboxylase (ACC). Efforts to screen and identify ACC inhibitors using flexible molecular docking resulted in Pinoxaden from Phenylpyrazole class as the most effective inhibitor with rerank = −81.436 and RMSD = 0.31.
    Authors:

  • Identification and characterization of foodborne pathogen Listeria monocytogenes strain Pyde1 and Pyde2 using 16S rRNA gene sequencing

    Journal of Pharmacy Research. Elsevier. Volume 6, Issue 7, July 2013, Pages 736–741
    August 2013
    Abstract
    Aim: Listeria monocytogenes acts as a pathogen for humans and animals, mainly causing, neonatal sepsis, abortions in pregnant females and severe infections such as septicemia and meningoencephalitis in susceptible hosts. Current study was aimed to identify novel strains of L. monocytogenes from retail chicken, beef meat and seafood samples.
    Methods: In order to identify the strain, extraction and amplification of genomic DNA, 16S rRNA sequence analysis was carried out. Phylogenetic trees were constructed using dnapars and dnaml available in Phylip. The secondary structures of 16S rRNA gene sequence were predicted using UNAFOLD, a Linux based software.
    Results: The results obtained were found to be a novel foodborne pathogens, which was further named L. monocytogenes strain Pyde1 and L. monocytogenes strain Pyde2, after characterization the sequence of isolate was deposited in GenBank with accession numbers ‘KC852899’ and ‘KC852900’ respectively. The Gibb's free energy of the secondary structures of L. monocytogenes strain Pyde1 and Pyde2 were −275.60 and −282.20 kcal/mol seems to be more stable in the present investigation.
    Conclusion: The described results of phylogenetic distinctiveness and phenotypic disparities indicate that strain 2b represents a novel strain of foodborne pathogens within L. monocytogenes species, for which the name L. monocytogenes strain Pyde1 and L. monocytogenes strain Pyde2 is proposed.
    Authors:

  • Screening of Bacillus anthracis Plasmid Px01 Proteins to Identify Novel Antigenic Peptides-an Immunoinformatics Approach

    European Journal of Biological Sciences 5 (3): 68-76
    May 2013
    Bacillus anthracis is a gram positive bacterium and the etiologic agent of anthrax, a common disease
    of livestock and, occasionally, of humans and the only obligate pathogen within the genus Bacillus. Hence the
    aim of the current study was to identify the novel antigenic peptides from the whole plasmid PX01 proteins of
    Bacillus anthracis. The plasmid proteome were analyzed using various online bioinformatics algorithms.
    The current study performed based on two facts i) the toxicity of B. anthracis is by secretion of exotoxins
    encoded from plasmid pX01 into the host cell and ii) the plasmid pX01 has a distinct 70kbp region. Hence the
    work was initiated by considering the proteins that are secreted out of the B. anthracis cell via the classical
    pathway. The proteins were analyzed for the transmembranes, antigenecity and their regions followed by
    two protein blasts across the human and bacillus database. The blast against the human database showing
    their absence in humans confirmed their antigenecity for humans and blast across bacillus had shown the
    B. anthracis specificity. The complete plasmid genome had 1695 protein entries at the genbank. At the end 10
    potential proteins were found using the Bioinformatics algorithms. During the process two other observations
    were found, one showing an antigenic protein sequence specific to nearly 100 Bacillus species and the second
    was a protein sequence that had low similarity for the well-identified breast cancer gene BRCA1.
    Authors:

  • Screening of Bacillus anthracis Plasmid Px01 Proteins to Identify Novel Antigenic Peptides-an Immunoinformatics Approach

    European Journal of Biological Sciences (EJBS)
    March 2013
    Bacillus anthracis is a gram positive bacterium and the etiologic agent of anthrax, a common disease
    of livestock and, occasionally, of humans and the only obligate pathogen within the genus Bacillus. Hence the
    aim of the current study was to identify the novel antigenic peptides from the whole plasmid PX01 proteins of
    Bacillus anthracis. The plasmid proteome were analyzed using various online bioinformatics algorithms.
    The current study performed based on two facts i) the toxicity of B. anthracis is by secretion of exotoxins
    encoded from plasmid pX01 into the host cell and ii) the plasmid pX01 has a distinct 70kbp region. Hence the
    work was initiated by considering the proteins that are secreted out of the B. anthracis cell via the classical
    pathway. The proteins were analyzed for the transmembranes, antigenecity and their regions followed by
    two protein blasts across the human and bacillus database. The blast against the human database showing
    their absence in humans confirmed their antigenecity for humans and blast across bacillus had shown the
    B. anthracis specificity. The complete plasmid genome had 1695 protein entries at the genbank. At the end 10
    potential proteins were found using the Bioinformatics algorithms. During the process two other observations
    were found, one showing an antigenic protein sequence specific to nearly 100 Bacillus species and the second
    was a protein sequence that had low similarity for the well-identified breast cancer gene BRCA1
    Authors:

  • Comparative modeling of 3-oxoacyl-acyl-carrier protein synthase I/II in Plasmodium falciparum– A potent target of malaria

    IJBR [INTERNATIONAL JOURNAL OF BIOINFORMATIC]
    January 2009
    Plasmodium falciparum causing malaria is yet reigning against drug design community when it
    comes to survival and defense. Continuous evolution and drug resistant character is foremost basis of
    parasite’s versatility. 3-oxoacyl-acyl-carrier protein synthase I/II in Plasmodium falciparum is discovered
    decisive in fatty acid synthesis machinery. Objectives of enzyme inhibition need structural characterization
    from its 3D structure. In present studies molecular modeling of 3-oxoacyl-acyl-carrier protein synthase I/II is
    achieved using in silico comparative modeling. ICM Molsoft algorithm was adopted for comparative
    modeling which provides an accurate and efficient module to build loops and side chains found non-identical
    in sequence. Energy parameters fell in thermodynamically stability zone. Modeled structure revealed
    appreciable measures when validated. Ramachandran plot signified the present work undertaken through
    conformational parameters ? (phi) and ? (psi) angles calculated from model with 83.2% residues in most
    favoured region. Further PROCHECK results confirmed acceptance of model through main and side-chain
    values. Root mean square distance of planarity found below 0.01. Beside some bad contacts, bond angles
    and bond lengths confer qualitative part of work. Structure of 3-oxoacyl-acyl-carrier protein synthase I/II can
    be important tool for structure based drug designing techniques to impel the search of new efficient
    inhibitors. Comparison of similar structures of parasite can further reveal mutational trends to study their
    evolution patterns.
    Authors:

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