Ashwani Kumar

Ashwani Kumar
Sir Ganga Ram Hospital | SGRH · Institute of Medical Genetics and Genomics

B.Sc, M.Sc, M.Tech, Ph.D.
Assistant Professor

About

29
Publications
28,161
Reads
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83
Citations
Introduction
Presently, I am engaged in R & D related to exome and whole genome sequence analysis to characterize undiagnosed disease in India using Bioinformatics approach.
Additional affiliations
May 2018 - present
CSIR - Institute of Himalayan Bioresource Technology
Position
  • Research Associate
July 2013 - September 2018
Jaypee University of Information Technology
Position
  • Researcher
July 2011 - May 2013
Jaypee University of Information Technology
Position
  • Research Assistant
Education
July 2006 - June 2008
University of Allahabad
Field of study
  • Bioinformatics

Publications

Publications (29)
Article
Full-text available
Alzheimer’s disease (AD) is an insidious, multifactorial disease that involves the devastation of neurons leading to cognitive impairments. Alzheimer’s have compounded pathologies of diverse nature, including proteins as one important factor along with mutated genes and enzymes. Although various review articles have proposed biomarkers, still, the...
Article
Full-text available
Formation of mature miRNAs and their expression is a highly controlled process. It is very much dependent upon the post-transcriptional regulatory events. Recent findings suggest that several RNA binding proteins beyond Drosha/Dicer are involved in the processing of miRNAs. Deciphering of conditional networks for these RBP-miRNA interactions may he...
Article
Full-text available
Identifying the factors determining the RBP-RNA interactions remains a big challenge. It involves sparse binding motifs and a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites in RNAs using an ultra-fast inexact k-mers search for statistically significant seeds. The seeds work as an anchor to...
Preprint
Full-text available
Identifying RBP binding sites and mechanistic factors determining the interactions remain a big challenge. Besides the sparse binding motifs across the RNAs, it also requires a suitable sequence context for binding. The present work describes an approach to detect RBP binding sites while using an ultra-fast BWT/FM-indexing coupled inexact k-mer spe...
Article
Background: Datura stramonium L. is widely used across the world for its therapeutic potential to treat inflammatory disorders. The current work was designed to isolate and identify steroidal lactones from D. stramonium leaves and evaluate their anti-inflammatory and analgesic properties. Methods: Several compounds were isolated from D. stramonium...
Article
The life challenging COVID-19 disease caused by the SARS-CoV-2 virus has greatly impacted smooth survival worldwide since its discovery in December 2019. Currently, it is one of the major threats to humanity. Moreover, any specific drug or vaccine's unavailability against COVID-19 forces discovering a new drug on an urgent basis. Viral cycle inhibi...
Article
Objectives The study was aimed to evaluate the potential of hydroalcoholic extract of Pinus roxburghii (PRE) stem bark in post-menopausal osteoporosis and its underlying mechanisms. Methods In silico docking of the markers was done using AutoDock version 4.2. for molecular targets: receptor activator of nuclear factor-κB (RANK), osteoprotegerin (O...
Preprint
Full-text available
Background: In-spite of ubiquitous expression of DROSA/DICER, miRNA formation and maturation are highly spatiotemporal implying involvement of other factors in their biogenesis. Several key studies have elucidated functions of few other RNA-binding proteins (RBPs) in miRNAs biogenesis, making it necessary to look miRNA biogenesis models with fresh...
Preprint
Full-text available
The recent outbreak of severe acute respiratory syndrome (SARS) coronavirus (CoV)-2 (SARS-CoV-2) causing coronavirus disease (covid19) has posed a great threat to human health. Previous outbreaks of SARS-CoV and Middle East respiratory Syndrome CoV (MERS-CoV) from the same CoV family had posed similar threat to human health and economic growth. To...
Article
Alzheimer’s disease (AD) is an age-related, non-reversible, and progressive brain disorder. Memory loss, confusion, and personality changes are major symptoms noticed. AD ultimately leads to a severe loss of mental function. Due to lack of effective biomarkers, no effective medication was available for the complete treatment of AD. There is a need...
Article
Full-text available
Background: Cholinesterase inhibitors are the first line of therapy for the management of Alzheimer's disease (AD), however, it is now established that they provide only temporary and symptomatic relief, besides, having several inherited side-effects. Therefore, an alternative drug discovery method is used to identify new and safer 'disease-modify...
Article
Full-text available
Podophyllotoxin is a high value metabolite having anticancerous activity and procured from a medicinal plant Podophyllum hexandrum. The escalating demand for podophyllotoxin necessitates development of alternate production platforms. Cell cultures have been tried in the past, however, podophyllotoxin yields were very low (0.3%). Multiple genes of b...
Poster
Full-text available
Genome-wide transcription profiling is a powerful diagnostic technique applied to disease tissue that may reveal quantitative and qualitative alterations in gene expression, that give information about genetics of disease. However, the data obtained from high-density microarrays and their mining is highly complex. In this paper, analysis of Hippoca...
Conference Paper
Deciphering the underlying mechanisms of all complex interactions involved in different signaling pathways is a pivotal step in the dissection and study of network-based data. Heuristic statistical solutions are conventionally used across the world to derive a meaningful perspective of the network based data by identifying related biological networ...
Article
Alzheimer's disease (AD) is a progressive, incurable and terminal neurodegenerative disorder of the brain and is associated with mutations in amyloid precursor protein, presenilin 1, presenilin 2 or apolipoprotein E, but its underlying mechanisms are still not fully understood. Healthcare sector is generating a large amount of information correspon...
Conference Paper
Full-text available
Aim: Aim of the present study was to screen out commonly consumed dietary natural compounds for their potential to alleviate diabetes and its associated complications and compare them with commercially available antidiabetic drugs. Methods: We screened ascorbic acid, gallic acid, quercetin, caffeine, ellagic acid, cinnamic acid and piperine throu...
Conference Paper
Full-text available
Biological processes are very complex and to understand them appropriately, there is a need for an interdisciplinary knowledge from diverse research areas such as systems and molecular biology. Systems biology endeavors to study, analyze and understand intricate biological systems by applying an integrated systems view using computational methodolo...
Conference Paper
ABSTRACT Background Alzheimer’s disease(AD) is a progressive, incurable and terminal neurodegenerative disorder of brain and is associated with mutation in Amyloid Precursor protein(APP), Presenilin1(PS1), Presenilin2(PS2) or Apolipoprotein E(APOE) but its underlying mechanism are still not fully understood. Healthcare sector is generating a large...
Article
Soybean Marker Database (SMDB) is a repository of important genomic information for soybean. At present several genomic databases are available for plants. Some of the important oilseeds plant databases are ATPID database, Castor Bean Genome Database, CGPDB, SoyBase, Legume Information System (LIS), Brassica database, Sinbase, etc. To gain comprehe...
Article
Full-text available
Quorum sensing (QS) is a process which allows a population of bacteria to coordinately regulate gene expression of their entire community. Bacillus subtilis is a soil organism which uses QS to alternate between competence for DNA uptake and sporulation. We propose a model to describe the components involved in QS and to analyze reaction species inv...

Questions

Questions (45)
Question
I have a query regarding Processing of Fastq to Ubam file and then to vcf.gz file, I followed  the same gatk guideline for conversion of paired end fastq files to .unmapped.bam files. and then used that unmapped bam file as input to GOAST server for further processing of Ubam file to vcf.gz format. but ever time my automated gatk job for conversion of ubam to *.vcf.gz is failed. I think there is problem in assigning Read group name to both paired end fastq.gz files during conversion of raw unmapped fastq.gz files to uBam file. Please give suggestion regard this.
Question
There are many tools available for germline CNV detection of WES and WGS data. But my question is which tool is best among them with maximum number of citation
Question
I want to extend my MD job from 100ns to 200ns. what changes should be applied in md.mdp and .tpr file and my another question is that usually how much time will be taken by the server of 64 processors to complete MD job of 200ns
Question
Hi, I want to run Production MD on a cluster by using Gromacs 2018.1. How to install this version in the cluster and run the process through qsub
Question
Hi everyone, during execution of gromacs when I perform step for ionization of protein system using ions.mdp file thaen following warning arises
"Too many warnings. If you are sure all warnings are harmless, use the -maxwarn option"
How to overcome this problem?
Question
I used LigParGen server to generate ligand topology but I dont know what changes I have to do in .itp file. when I issued this command: >gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tor I faced this error:ERROR 1 [file LIG.itp, line 11]: Atomtype opls_800 not found I checked the aminoacids.rtp file of /usr/local/gromacs/share/gromacs/top/oplsaa.ff and found there is not atomtype opls_800 and 801 and ... in this file. while the LIG.itp which generated by LigParGen server has atomtype opls_800 , 801 and ... . I have to modify all of these atomtype opls_ in order to correspond to with aminoacid.rtp file? I would be thankfull if you help me.
Question
How to automate javascript in HTML DOM,so that multiple CSV file can generate graph from coordinate position of each approx. 150 RBPs in each 1881 miRNA
Question
I have a pdb file of docked complex of protein-RNA complex from patchdock, How to generate 2D interaction plot through ligplus+. sample file are attached with this question.
Question
I have a pdb file of docked complex of protein and ligand from patchdock, but there is an error occurring when I am importing it to LigPlot.
Question
I have approx. 150 protein ligands and want to dock all 150 protein ligand on single RNA at a time. Is there any tool available for this particular purpose.
Question
I need to integrate an existing neo4j-database into my django project using your package. Is there any best practice or things I need to consider to do this?
Question
I want to generate subnetwork from whole network generated using D3.JS library of javascript. I want to know is any other tool available for network generation or for module search.
Question
I built a database containing 23 tables of different sample according to condition. Each table contain same column name with different values. How to write join sql query to retrieve data from all tables.
Question
I have a multiple checkbox (about 40) in search form of my website. This checkbox contain names of tables stored in database. I am unable to fetch data from columns of the tables in database by clicking on multiple checkbox. Need useful suggestions and solutions

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Projects

Projects (2)
Archived project
MOTO Promotion of Science and Technology: The main moto behind the establishment of this NGO is to promote Science Education & Technology planning and promotion among the poor student of India, studying in the small town and village; especially those who are studying Science subject and even not aware fully about the Science and Technology. But along with Science and Technology promotion, this NGO will also equally participate in the promotion and betterment of agriculture and health-related issues all over India mainly focused on small-town and rural populations. VISION ISET FOUNDATION’s vision is to be support and platform to motivate students and society toward science and energize toward innovation in field of science and technology. MISSION Facilitate excellent scientific education & awareness and promotion of innovation, entrepreneurship, competitiveness, and stewardship toward science in our society. Our Believes • In transparency • In Charity with Dignity • In professionalism and dedication Area of Operation The area of operation shall be all over India especially suburban and rural areas and our focus will be on science education-related issues. OBJECTIVES- 1. To promote scientific education in high school and intermediate standards. 2. To improve more thinking of students towards science. 3. To implement and co-ordinate various projects aimed towards the promotion and development of science and technology. 4. To establish a science library and reading rooms in semi-urban and rural areas. 5. To create Training/education centre and health centre 6. To provide scholarship/Financial help to poor rural/village students for their science academic promotion 7. To make efforts for the overall promotion of science and technology in society. 8. To establish and run various Welfare Centers to promote de-addiction, welfare of senior citizens, physically and mentally handicapped persons and overall human development; 9. To establish, manage and run high-level Training Centers to bring out personalities in the fields of science education. 10. To work on projects for medical care and health developments using new technologies and inventions. 11. To organize and conduct programmes on scientific education, health’s sanitation and nutrition among poor children. 12. To implement projects for the development of agriculture in a scientific way. 13. To implement projects for the promotion of scientific techniques in semi-urban and rural areas. 14. To organize lectures, seminars, conferences, workshops, study groups, debates, symposia and other programmes at international, national, regional and state level to develop innovative ideas towards science education and technologies. 15. To accept donations, grants, presents, gifts and other offerings in the shape of movable or immovable properties and the same shall be utilized for the promotion of scientific education and technology. 16. To implement projects for start and run Science Institutes for scientific Studies at semi-urban and rural areas. 17. To implement projects to edit, translate, publish book, pamphlets, periodicals, science posters, educative and informative material that may be considered desirable for promotion of science. 18. To enhance the interaction between scientists (of India as well abroad from different field of Science) and motivated students. 19. To provide a channel for laboratory scientists and technologists to interact with rural life and its realities thus enabling them to learn from the accumulated knowledge of the villagers’ traditional methods, so that the scientific basis of such knowledge of the ages is understood and its technological improvements attempted. 20. To provide a forum for rural innovators to interact with science and technology experts, so that they imbibe the scientific method in their work, when appropriate, and encourage the multiplication of innovative endeavors. 21. To conduct short term training programmes for rural people to implement science technologies in routine life.
Project
Major Goal of my Project is to find efficient biomarkers which can be helpful for early detection of multistagial complex neurodegenerative disease i.e Alzheimer's Disease for proper treatment. To find inhibitors for the key enzyme of brain neurotransmitter.