Ming Tommy Tang

Chatomics! — The Bioinformatics Newsletter Why Subscribe?✅ Curated by Tommy Tang, a Director of Bioinformatics with 100K+ followers across LinkedIn, X, and YouTube✅ No fluff—just deep insights and working code examples✅ Trusted by grad students, postdocs, and biotech professionals✅ 100% free

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10/ AI gives you speed. You bring the judgment.

Double-check its code. Validate its logic. Ask better questions.

The future belongs to the curious--especially those who type well.

9/ Ask AI to:
- Explain PCA vs UMAP
- Write a bash loop
- Compare ChIP-seq vs ATAC-seq
- Draft a Seurat filtering function

Then verify everything it gives you.

8/ Will AI replace biologists? No.

But if you're a biologist who doesn't use AI, you're already falling behind.

It's never been easier to learn genomics, statistics, or scripting.

7/ These are the types of questions AI handles well.

Quickly. Clearly. Not perfectly--but better than flying blind.

6/ Another question: why is only 0.1% of ChIP-seq input used?

Short answer: input DNA is plentiful. ChIP DNA is scarce--you're only pulling down what's bound to the protein of interest.

AI explained this in 10 seconds.

5/ Someone asked me: why calculate the TSS enrichment score for ATAC-seq?

Years ago, I'd dig through papers for hours.

Now I ask AI to explain it simply, then go deeper myself.

4/ Even as an experienced bioinformatician, I still use AI daily.

Why? Because it helps me think faster, not lazier.

3/ Now? You ask ChatGPT, Claude, or Gemini.

You get a decent answer in seconds.

That's not magic. That's leverage.

2/ In 2013, if you had a problem, you went to Biostars or StackOverflow.

You waited days. Or searched for hours.

1/ AI won't replace you.

But a biologist who uses AI will.

Especially in bioinformatics, where the questions never stop coming.

Immunosuppressive mechanisms and therapeutic interventions shaping glioblastoma immunity www.nature.com/articles/s4...

Chatomics! — The Bioinformatics Newsletter Why Subscribe?✅ Curated by Tommy Tang, a Director of Bioinformatics with 100K+ followers across LinkedIn, X, and YouTube✅ No fluff—just deep insights and working code examples✅ Trusted by grad students, postdocs, and biotech professionals✅ 100% free

I hope you've found this post helpful.

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5. 42basepairs 42basepairs.com/

4. Intervene: a tool for intersection and visualization of multiple gene or genomic region sets

bitbucket.org/CBGR/interv...

GitHub - gosling-lang/gos: A declarative interactive genomics visualization library for Python. A declarative interactive genomics visualization library for Python. - gosling-lang/gos

3. The goal of **g(r)osling** is to help you build interactive genomics visualizations with [Gosling](github.com/gosling-lan...). This package uses [reticulate](rstudio.github.io/reticulate/) to provide an interface to the [Gos](github.com/gosling-lan...) Python package.

GitHub - PhanstielLab/plotgardener Contribute to PhanstielLab/plotgardener development by creating an account on GitHub.

2. plotgardener is a genomic data visualization package for R. Using `grid` graphics, `plotgardener` empowers users to programmatically and flexibly generate multi-panel figures

github.com/PhanstielLa...

GitHub - crazyhottommy/scATACutils: R/Bioconductor package for working with 10x scATACseq data R/Bioconductor package for working with 10x scATACseq data - crazyhottommy/scATACutils

I used that to plot single-cell ATACseq tracks github.com/crazyhottom..., more examples rpubs.com/crazyhottom...

5 tools to visualize genomic datasets 🧵
1. Karyoploter bernatgel.github.io/karyoploter...

A pan-cancer compendium of 1,294 plasma cell-free DNA methylomes and fragmentomes enabling multicancer detection www.nature.com/articles/s4...

Chatomics! — The Bioinformatics Newsletter Why Subscribe?✅ Curated by Tommy Tang, a Director of Bioinformatics with 100K+ followers across LinkedIn, X, and YouTube✅ No fluff—just deep insights and working code examples✅ Trusted by grad students, postdocs, and biotech professionals✅ 100% free

I hope you've found this post helpful.

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Whimsical — Where great ideas take shape Whimsical is a collaborative whiteboard app for thinking and planning. Create flowcharts, mind maps, wireframes and more.

10. whimsical.com/

How to Draw Flowcharts With LaTeX | Baeldung on Computer Science Learn how to draw flowcharts with LaTeX/TikZ.

9. Latex www.baeldung.com/cs/latex-fl... if you are geeky

8. Lucidchart www.lucidchart.com/pages/ very similar to draw.io

7. DiagrammeR if you want to play with R rich-iannone.github.io/DiagrammeR/

GitHub - fredhutchio/inkscape-tutorial: A tutorial for the free Inkscape cross-platform vector graphics editor. A tutorial for the free Inkscape cross-platform vector graphics editor. - fredhutchio/inkscape-tutorial

6. Inkscape github.com/fredhutchio... I use it to make figures (it is free)

5. draw.io

4. Miro miro.com/aq/ps/flowc...

3. Adobe illustrator

Flowchart Maker - Create Online Flowcharts for Free | Figma Build diagrams quickly and easily with our Online Flowchart Maker. Share ideas, diagrams and processes with your team in realtime, in Figma, for free.

2. Figma www.figma.com/templates/f... recently bought by Adobe