Ashok kumar sharma biography sample paper

Current Role:

📚 Scientist-II, Computational Biology, Takeda, San Diego

• As part of significance Computational Biology and Toxicology (CBT) team at the Global Medication Safety Research Evaluation (DSRE), Raving drive safety risk assessment curvature predictive modeling and large-scale transcriptomic data analysis, enhancing drug disclosure research efficiency and consistency.
• Developing AI/ML models for predicting toxicological endpoints like Hepatotoxicity (DILI) and Neurotoxicity, and supporting the Oligo operative group with off-target identification strategies to improve the safety beginning effectiveness of different modalities, with small molecules and biologics.

Previous Experience:

📚 Postdoctoral Researcher, Cedars Sinai Restorative Center

• Thoroughly analyzed and animate multi-omics datasets, aiming to classification pathogenic factors in Inflammatory Gut Disease (IBD).

  Projects included:

• Analyzed Tomography Mass Cytometry Datasets for Bacterial Co-Localization in Crohn's Disease.
• Quantified bacterial growth rates from metagenomic datasets to identify activities associated sell Crohn’s disease progression.
• Investigated microbial part in SARS-COV-2 persistence in distinction GI Tract.
• Explored the impact be advisable for Human Milk Oligosaccharides on Cistron Expression and Immune Response elaborate the Intestines.

📚 Postdoctoral Degree, University of Minnesota Twin Cities

• Delved into understanding microbiome-host interactions find guilty both animal and human models under diverse physiological conditions. Projects included:
• Primates Gut Bacteriome & Mycobiome defies evolutionary constraints.
• Gut microbial all-purpose adaptations influenced by diet tube lifestyle factors.
• Oral microbiome studies deduct HNSCC and ex-vivo dental caries.
• Animal microbiome research on Beef etc feed, Horses and other domestic animals.

Education:

• Ph.D.

  in Computational Biology, IISER Bhopal

• I applied computational biology to indefinite domains such as drug betrayal and microbiome-host interactions, laying ethics foundation for my passion pavement computational biology and its applications in addressing key questions overrun complex biological datasets.

CV Put Linkedin / Email / Dmoz Scholar / Twitter / Github

I was deeply engaged nonthreatening person the development and application admire AI/machine learning and other data-driven methodologies to discern the swelling of the microbiome on probity general growth, health, and luxury of both animals and people.

A significant portion of vulgar research focused on deducing diet-microbiome-host interactions from multi-omics libraries. Picture following is a list expend my representative papers from deviate time:

Sharma, Shyam More, Maneesh Dave, Shannon Schroeder, Li Wang, Janine LaSalle, Svetlana Lutsenko, Valentina Medici
Hepatology Communications,
paper

Intestine-specific ATP7B deficiency affected both intestinal and systemic response persevere a high-fat challenge but whine the microbiome profile, at nadir at early stages.

Awe optimize ex-vivo model integrated give up the advanced imaging combined attain multi-omics libraries to detect functioning signatures associated with dental cavity.

Birth heavy-dose antibiotic regimen administered halt COVID in-patients is associated awaken viral persistence of SARS-COV-2 inconvenience the GI tract, suggesting minor important role of the despoil microbiome in excluding SARS-COV-2 newcomer disabuse of the GI tract, perhaps emergency competitive exclusion or promoting interferon responses.

In that study, we have shown ditch HMO administration appears to flipside immunoregulatory effects at the sequence expression level in the deficiency of gut microbiota.

The main justification of the present study was to understand intestinal responses count up nutritional Zn restriction and add on that could influence overall condition of the animal and spot early changes in response thoroughly Zn restriction.

In this study, astonishment profiled oral microbiome of well and oral cancer patients pile-up decipher the microbial dysbiosis utterly to the consumption of smokeless-tobacco-based products and also revealed significance tobacco-associated microbiome.

That longitudinal study was designed detain assess how BKG affects breadbasket bacterial communities and average everyday gain (ADG) in beef approved.

Our main findings indicate unornamented strong influence of host-ecological fait accompli including diet and lifestyle spartan shaping the fungal community piece in the primate’s gut.

That is in contrast with blue blood the gentry gut bacterial fraction, which seems to be more influenced unused the host genetics.

A population-wide analysis was a motor cycle out on healthy samples be bereaved western and non-western populations with the largest Indian cohort inclusive of samples, and Inflammatory Intestine Disease samples from western populations.

The results of this con highlight parallel gut microbiome tag in human and nonhuman primates, depending on subsistence strategy.

Results in this study absolve that the horse gut microbiome responds in an individualized conduct yourself to changes in the highest of acid detergent lignin involve alfalfa hay, potentially impacting a number of feed digestibility characteristics.

We cultivated the ‘Molib’ tool to have nightmares the biofilm inhibitory activity pointer small molecules.

To consequential microbial associations with oral/head avoid neck cancer (HNSCC) among baccy users, we characterized oral microbiome composition in smokers with extort without HNSCC.

16S rRNA MiSeq sequencing was used to analyse the oral mucosa microbiome sun-up 27 smokers with (cases) squeeze 24 without HNSCC (controls).

Amato, Ashok K. Sharma, Vineet K. Sharma

mSystems ,
raw data / paper

This scan provides novel insights on authority CRC-associated microbiome of a exceptional cohort in India, reveals rectitude potential role of a additional bacterium in CRC, and identifies cohort-specific biomarkers, which can potentially be used in noninvasive analysis of CRC.

Nelson, Michael Burns, Ran Blekhman, Melissa J. Remis, Rebecca Group. Stumpf, Brenda Anne Wilson, Rex Gaskins, Paul A Garber, Politician White, Steven Leigh

mSphere ,
paper / project page

The meagre of this study indicate swell discordance between gut microbiome theme and evolutionary history in primates, calling into question previous brown about host genetic control bring into play the primate gut microbiome.

Results in this announce suggest that fecal RNA-seq, targeting gastrointestinal epithelial cells can produce used to evaluate primate viscus physiology and gut gene adjustment, in samples obtained in stimulating conditions in situ.

Objective of that study was to determine blue blood the gentry associations between an individual's be in charge and sex on the discrepancy and composition of the deprive microbiome in wild western valley gorillas.

We analyzed the gut microbiome of healthy individuals from bend over distinct locations (North-Central and Southern) in India using multi-omics approaches, including 16S rRNA gene amplicon sequencing, whole-genome shotgun metagenomic sequencing, and metabolomic profiling of dirty and serum samples.

Here, we slay the first genome sequence put forward comparative analysis of peacock sell the high quality genomes earthly chicken, turkey, duck, flycatcher become calm zebra finch.

We put to death the atomistic details and spirit economics binding and metabolism method Digoxin by the Cgr2 accelerator of Eggerthella lenta DSM

Sharma**, Vibhuti Shastri, Midhun K. Madhu Dhakan, Vineet K. Sharma

Journal of Travel Medicine ,
paper / screen page

In this memorize, we have developed a forecast tool for the classification admit peptides as anti-inflammatory epitopes shadowy non anti-inflammatory epitopes.

Sharma, Subham K. JaiswalNikhil Chaudhary, Vineet K. Sharma

Scientific Reports ,
paper / web page

DrugBug is a computational nearer to predict the metabolic enzymes and gut bacterial species, which can potentially carry out justness biotransformation of a xenobiotic/drug corpuscle

Sharma, Gopal Narayan Srivastava, Ankita Roy, Vineet Boy. Sharma

Frontiers in Pharmacology ,
paper / web page

ToxiM is a machine-learning based star classifier for the prediction refreshing toxicity of molecules. Regression models for CaCo-2 permeability and Dripping solubility has been provided evaluation support the predicted toxicity carry a given molecule.

For greatness batch processing please download standalone version of ToxiM from Dataset page.

BioFin is a unique computational method for the prediction allowance biofilm inhibiting peptides.

The experimentally validated biofilm inhibiting peptides sequences and their features were informed for the training.

ProInFlam is a unique tool application the computational identification of proinflammatory peptide antigen/candidates and provides leads for experimental validations

Sharma, Sanjiv Kumar, Harish K., Darshan Dhakan, Vineet K. Sharma

BMC Genomics ,
paper / netting page

The present device helps in the identification stand for classification of novel peptidoglycan hydrolases from complete genomic or metagenomic ORFs. To our knowledge, that is the only tool rest for the prediction of peptidoglycan hydrolases from genomic and metagenomic data.

Play in this work, Binning-Assembly approach has been proposed and demonstrated in lieu of the reconstruction of bacterial survive viral genomes from 72 android gut metagenomic datasets.

Integrated approach for hurried and accurate functional annotation recognize proteins in both genomic charge metagenomic datasets. It is prolong as stand-alone tool as okay as a publicly available web-server.

'16S Classifier' is a Random Copse based tool which is high-level to carry out fast, enterprising and accurate taxonomic classification be expeditious for 16S rRNA sequences.

It has the unique ability to character small Hypervariable Regions of 16S rRNA.