STEMCasts®: From Transcriptomics to Therapeutics. Host: Ayush Noori, Researcher, Researcher at Mass General, Freshman at Harvard University (Recording available)

About this STEMCasts® episode:

The advent of the -omics age, coupled with the development of robust bioinformatics tools, has granted scientists a window into the molecular and cellular processes which are the root causes of human disease. Simultaneously, large patient datasets have been made publicly available via massive online repositories and are invaluable resources for bioinformatics students.

This STEMCasts® episode will teach students the fundamental skills necessary and inspire a
passion for future explorations in bioinformatics. Due to the extensive nature of the material, the webinar will be 2 hours. We will also host a special Q&A session with renowned expert Dr. Sudeshna Das, Assistant Professor of Neurology at Harvard Medical School.

Meet Your Instructor:

Ayush Noori is an incoming freshman at Harvard University and student researcher finding solutions for intractable contemporary problems. Dedicated to advancing the fight against neurodegeneration and galvanizing tomorrow’s scientists. Fostering compassion and empathy in the lives of those around him.

Ayush is also the Boston Chapter Founder of EduSTEM, an youth led international organization with a motto of ‘Educate, encourage and empower’.


What You’ll Learn:

  • Fundamental skills necessary for future explorations in bioinformatics.
  • The history of and biology behind the transcriptomics revolution, from microarrays to next generation sequencing to the future of third generation sequencers.
  • How to perform introductory bioinformatics analysis on datasets from the Gene Expression Omnibus. (GEO, https://www.ncbi.nlm.nih.gov/geo/)
  • Real-world case studies of using transcriptomics to better patient healthcare.


Target Audience:

  • Advanced middle school, high school, and college students interested in bioinformatics or data science.
  • Students should have previously taken an introductory biology course.


STEMCasts® Schedule:

  1. Introduction and Overview
    • Overview of workshop schedule.
    • What sparked my own passion for neuroscience and bioinformatics?
    • How can students become involved in impactful research, even with limited resource availability?
    • What distinct advantages are offered by bioinformatics over wet lab science?
    • What are some drawbacks that every bioinformatician must consider before drawing conclusions from their data?

  2. Biology Background
    • All about genes, DNA, and RNA! Overview of transcription and translation.
    • How do cells respond to environmental and endogenous stimuli?
    • How does the transcriptome govern the function of a cell?
    • What are the differences between the transcriptome and the proteome?
    • What can we discern about biological function from transcriptomic datasets?
    • Studying non-coding RNAs and their influence on cellular function.

  3. History of the Transcriptomics Revolution
    • Overview of RNA extraction, reverse transcriptase, cDNA libraries, and expressed sequence tags (ESTs).
    • Sanger sequencing – serial analysis of gene expression (SAGE), cap analysis of gene expression (CAGE), and massively parallel signature sequencing (MPSS).
    • The advent of microarray technology via complementary hybridization.
    • Spotted oligonucleotide arrays and Affymetrix high-density arrays.
    • The rise of RNA-seq technology from 2006-2008.

  4. Data Analysis of Transcriptomics Data
    • Differential expression analysis of microarray data using example datasets from the Gene Expression Omnibus.
    • Differences between RNA-seq and microarray analyses.
    • Mapping to pathway databases (Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, etc.) and exploring intra-pathway interactions.

  5. From Transcriptomics to Therapeutics
    • How can transcriptomics data help us identify new biomarkers and therapeutic targets for patients?
    • Examine real-world case studies of using transcriptomics to better patient healthcare.



Reply to this topic with questions and feedback. This webinar is part of a STEM-Away® Pathway in Bioinformatics.


stemcasts-bio1 (2)

7 Likes

I was not able to make the Zoom call today. Will there be more?

The recording will be made available shortly.
Also, more material will be shared with the Bioinformatics-1 Group

First of all, I want to say that this webinar was extremely intriguing and helpful! Thank you, Ayush.

I believe it is easy to ignore the emotional aspect of researching diseases simply because at face level, it seems like a chart of numbers, not a life. Ayush, right off the bat, alluded to this and backed it up with facts (5.8M individuals with Alzheimer’s in the US!). It was very humbling and reminded me of why I want to enter the STEM field.

It was nice to listen to Ayush talk about the biology behind genes. Having taken many biology courses, his concise summary was just enough information to understand the data analysis (something that is not my strong suit).

I have personally had the pleasure of taking part in some of the wet lab procedures he mentioned in this webinar (western blot and RNA extraction). Seeing this translated into useful mass data was so cool!

The best thing I learned from this video was about the Omnibus data resource. I paused it and went on a 2-hour bender looking at different diseases and the data behind it. It also amazes me that conclusions can be made from a large set of data. I also appreciate how Ayush mentioned that the lack of random sampling leads to fraudulent/incorrect results. Research truly is a multi-subject language that requires a comprehensive understanding of results, how they were taken, and how to interpret them.

I know the least about programming and coding. However, watching Ayush explain a step-by-step differential analysis of sample data was extremely helpful.

I am excited to learn more about bioinformatics.

1 Like

Thank you for the very thoughtful and insightful reply! It is great that you have started exploring the Omnibus data. You will feel much more comfortable taking the next steps when the project begins. Welcome to STEM-Away :slight_smile:

1 Like

I just wanted to write a quick reply back to Ayush because I connected with him on LinkedIn looking for more feedback about the Omnibus data tool. His helpful insight has allowed me to find relevant research for my Master’s thesis! Keep up the good work Ayush!

Thanks Alex! Glad I was able to help out. @AlexG5353

1 Like

Great to hear from you, Angelina! Thanks for the positive feedback. It looks like you’re on the right track; feel free to reach out to me if you have any additional questions! @awprakas