Leaders in Pharmaceutical Business Intelligence (LPBI) Group

Vaishnavee R. Joshi, BSc, MSc, Research Associate 3, Medical Text Analysis using NLP and Synthetic Biology

Roles at 2.0 LPBI

• Member of the Team: Medical Text Analysis using NLP, ML-AI

Series E, Volume Four: Medical 3D BioPrinting – The Revolution in Medicine, Technologies for Patient-centered Medicine: From R&D in Biologics to New Medical Devices

Editors: Larry H Bernstein, MD, FCAP and Aviva Lev-Ari, PhD, RN

https://www.amazon.com/dp/B078QVDV2W

Available on Kindle Store @ Amazon.com since 12/30/2017

URL on our Journal

https://pharmaceuticalintelligence.com/biomed-e-books/series-e-titles-in-the-strategic-plan-for-2014-1015/volume-four-medical-3d-bioprinting-the-revolution-in-medicine/Link to the Book on our Journal

Volume Four: Medical 3D BioPrinting – The Revolution in Medicine

BioMed e-Series

Selected 12 Research Categories from the Journal Ontology include the following:

The topics that I would like to gain knowledge and work experience in:

• Bio printing in regenerative medicine
• Micro engineering cell-tissue and system
• Drug development using multi organ chip
• Drug development formulation using 3-D printing
• Organ on a chip
• BIO MEMS
• Programmable sensors
• 4-D printing and meta materials
• Automated cell processing
• AI, NLP, deep learning in various medical technologies and biology
• Biological engineering
• Nuclear medicine

Master Thesis

Sc-RNA sequence analysis of ageing related disorder fibroblast priming

Abstract:

Ageing is a multifactorial process associated with multiple mechanisms,one of which include fibroblast priming it is a process in which eradication of fibroblast cell present in the dermis layer takes place causing ageing of skin cells (Apoptosis). The advent of – single cell transcriptomics technologies is now allowing a window to unleash the preclusive factors responsible for such physiological changes at molecular and cellular level. Showcasing the cell level analysis of 5 samples taken from different age groups reveals the cell clusters showing differential expression variation in the respective samples. Normalization of 25,000-30,000 cells from each sample divulge potential cell clusters that might be involved in fibroblasts functional annotations. These findings are boosting factors for future cell type analysis, gene marker identification, modeling of the network of fibroblasts priming and understanding human skin aging and its associated phenotypes.

Keywords: Single cell technology, Transcriptomics, Aging, fibroblast, Modeling.

Objective

• Noise reduction and obtaining quality reeds
• Mapping quality reeds with annotated human reference genome
•  Obtaining the Differential expression analysis of aligned genes and predicting cell types using clustering
• Analysis , interpretation and visualization

Methodology

1. Selection of dataset, uploading the samples on Galaxy

2. Quality control for the raw data using tools such as FASTQC and trimgalore

3. Mapping of the quality reads using RNA-STAR solo a equivalent method for 10X chromium pipeline  

4.  Assessing the mapping quality with MultiQC tool

5. Downstream analysis for cell level evaluation paradigms including trajectory analysis

6. Cellular trajectory inference and branching.

Conclusion

An ideal pipeline following the 10X chromium agenda was performed for each sample separately. The two samples that are sample 7 and sample 9 were prone to less cell expression count hence the differential expression and clustering was not achieved due abnormalities and threshold of cells in the count matrix. But the samples 8, sample 6, sample 10 have an applicable threshold count that led to differential expression and clustering of the cells. Accounting to the downstream analysis of these samples clusters that represented higher count of gene expression were interpreted and cell type analysis was done successfully but the trajectory and network analysis was done for sample 6 only due to high gene matrix count. These study will help in identifying the cell types in the samples collected and identify molecular marker that will be used in modeling and simulation studies in the future for the amendment of ageing related disorder.

BIO

Vaishnavee R. Joshi

   Vaishuvj3124@gmail.com  |+91-7020771927 | linkedin.com/in/vaishnaveejoshi

Career objective:

A highly organized and hard-working individual looking for a responsible position to gain practical experience in fields such as systems biology, synthetic biology, AI, functional genomics and pharmaceuticals.

Education:

Mahatma Gandhi Mission (MGM) university, Maharashtra India

Master of Bioinformatics                     June 2019-August 2021 

Institute of Biosciences and Technology

• Attended various conferences on bioinformatics, Genomics, Proteomics.
• CGPA: 8.9

• Dr. Babasaheb Ambedkar University (BAMU), Maharashtra India.

Mahatma Gandhi Mission (MGM) university, Maharashtra India

Bachelor of Bioinformatics                         June 2016-April 2019

Institute of Biosciences and Technology               –

• Completed and passed with First Distinction.
• Participated in various competitions like poster presentation, tableau work.
• CGPA: 7.3  
• 12^th standard  (HSC)  Board                           2014-2016

Deogiri College Aurangabad

70%

• 10^th standard  (SSC) Board                                 2014

Saint Francis De ’sales High school, Aurangabad Maharashtra

     84%

Skills:

Technical skills (Computational):	Microsoft office, linux commands, Data analysis, Database management, shell scripting
Languages:	C, C++, java, Python, Perl, R.
Interpersonal:	Active and quick learner, listening, Assertiveness, Problem-solving, collaborative, organized and strategic planner.
Other (Bioinformatics skills)	Machine learning, biological databases, Big data, AI, Galaxy and other tools, sequencing analysis, computational molecular biology.

EXPERIENCE:

1. Data Analyst                                                                    10/12/19–1/4/20

  ICON Centre and hospital

• Compiling and analyzing test data generated by DASII for early identification of children who are at risk of learning disorder.
•  It involved working on large data frame with almost 3000 children’s data.
• Modeling of factors responsible for learning disorder and using statistical methods to line up methods of prediction of same

PROJECT:                  

1. Design and development of algorithm for cell behavior (Still in the process)-In-Silico project

• Learned the cellular processes of all prokaryotic cellular organelles.
• Strategically designed the algorithm for the cellular processes such as DNA replication.

2. Bacterial diversity analysis (Still in the process)-Wet lab project

• Collected samples from sources such as Air, water, and soil. Separate cultures were made for all samples.
• Isolation of DNA was performed using electrophoresis on all samples with diversity analysis.

3. Single-cell RNA sequence analysis of aging related mechanism fibroblast priming

• Analysis of single cell RNA sequence data using R and galaxy tools
• Quality control and pipeline designing for data
• Differential analysis and integration using Seurat for 25,000 cells
• Future prospects to design new therapeutics for aging process

ACTIVITIES :

1. “AGE OF BIOTECHNOLOGY  ” (31^st jan -1^st feb 2017 )  organized by MGM’s IBT Aurangabad
2. 1^st National symposium “AGE OF BIOINFORMATICS ”( 11-12 September 2017) organize by MGM’s IBT Aurangabad
3. Seminar on “cognitive technology” (august 05^th 2017)organize by PPCRC Puna Maharashtra
4. Workshop on “Artificial Intelligence” (14^th September 2018) organize by PPCRC and MGM IBT Aurangabad ,Maharashtra .
5. The symposium on “Accelerating biology 2020” (04-06,2020) organize by C-DAC, Pune Maharashtra

Reference:  Dr. Sanjay Harke   Mail: sanjay.harke@gmail.com

                                            

Name                        : Vaishnavee Renukadas Joshi

D.O. B :                      : 24/11/97

Language Known      : Marathi, Hindi, English.

Gender                       :  Female

Nationality                 :  Indian

Marital status            :  Unmarried