The advances of genomics:

From single genome to pan-genome

Songtao Gui
2022-09-23



Table of contents

  • What I have done: single ref. => pan ref.

  • Things help to know me

  • What quality I think make yourself happy




The academic part:

From single genome to pan genomes

Tech Expansion
Tech Expansion => Data Expansion

The limitations of single reference genome

πŸ‡ Limitations of one ref 1: Alignment bias: variant calling bias
2: Missing info of NON REF seqs

Call for Pan genome




Researches during my PhD


Get on the bus of genetics and genomics

PhD: I study lotus

PhD: Reveal the lotus genomes

Lack all level of genomes and genetics information for lotus




What I got during PhD

  • Get familiar with bioinformatics, genomics, pop-genetics

  • Experiences of scientific writing and being rejected

  • Extra time to arm myself (and met my wife)




Researches duing PostDoc

On the way of omics integration and pan-genomics

Goals:

  • Integrating Multi-omics data => a database

  • Generating more omics data => sequencing

  • Construct maize/Zea pan-genome

  • Maize genetic variation map

All lead to:better understanding of \( V_{geno} \sim V_{pheno} \)




ZEAMAP database







Pan-Zea genome and maize genetic variation map







The chat part:

What made me me

What brought me here (academic, bioinformatic)

Why Bioinformatics

  • Small Lab (~10 members), little fundings, big happiness;

  • He REALLY loves teaching;

  • Has little academic ambition, but he'll make his best to help ours;

  • He make sure we do not cheat, we get ourselves graduated;

My Highs and Lows

  • PhD 5.5 year: No pressure
  • PosDoc Year 1 & 2: ZEAMAP, pan-Zea
  • PosDoc Year 3: COVID, Redo-ZEAMAP
  • PosDoc Year 4: COVID, family, pan-Zea
  • PosDocYear 5: I make peace with myself, and I don't think too much


    • What is important to stick to academic, without being too frustrated?

    My answer is:
    Don't think too much, and find and keep mind flow state as long as possiable.

    Back to the question of Why academic:

    I don't want to deal with people at work You cannot avoid dealing with people.
    I thought science is beyond humanity Yes, but scientists are humans
    More likely to do what I like πŸŒ™ while still making 🍞 Most time, you did not do what you like, or the way you like


    So, why (still stick to) academic?

    θ·ŸεƒιΊ»θΎ£ε°ιΎ™θ™ΎπŸ¦δΌΌηš„, θΎ£ζ˜―ηœŸηš„θΎ£, δ½†ηˆ½ζ˜―ηœŸηš„ηˆ½ε•Š!

    Thank You!


    Follow ME

    My GitHub: https://github.com/SongtaoGui

    My Blog: https://songtaogui.github.io/