Simona Cristea Profile picture
Oct 31, 2022 12 tweets 4 min read Twitter logo Read on Twitter
It’s that time of the year🎃when students are deciding if to apply for #PhDpositions👻

Even though #Academia is far from perfect:doing a #PhD is valuable.

It develops unique & important skills that will stay with you forever

These PhD skills are totally☹️not discussed enough👇 Image
1. Ability to work interdependently🔁(independently & with others).

Doing a PhD requires individual planning, as well as collaborating and working within teams. The ability to dive really deep into both these areas *simultaneously* is one of the defining features of a PhD.
2. Self-motivation & drive

Doing a PhD can also be hard & frustrating😮‍💨. You'll sometimes find yourself working alone, with no clear goals on the project, and no end in sight.

Making it work somehow nurtures your ability to motivate yourself when faced with hard situations.
3. Versatility & adaptability

When starting, you don't know where your PhD will take you. You'll have to be adaptable, and change & refine your ideas over and over again, until you find a hypothesis that you are happy with pursuing.
4. Resilience

But even after you find a golden idea💡you are excited about, it will almost certainly not work from the first go!

Sometimes not even from the second, nor third, nor tenth. You'll need to keep trying, troubleshoot & think about the problem in different ways.
5. Ability to learn quickly

During a PhD, you learn a lot📚. Mostly by yourself & mostly from scratch. This means your PhD will also teach you how to learn. Always being ready to learn new things keeps your brain fresh & helps you be happier. It's one of the greatest gift.
6. Problem solving

A PhD involves by definition solving a hard problem. Hadn't it been hard, it wouldn't be (unsolved) science, and it wouldn't take you 4+ years to do it.

Methodically formulating & dissecting the problem you are faced with are domain-independent skills.
7. Ability to synthesize

A PhD means pushing the boundary of knowledge. This automatically means you need to know what knowledge means, such that you can push it forward. This further means you need to understand a huge body of knowledge and extract its essence.
8. Decision-making

During your PhD, you'll face many crossroads. For most of them, there'll be no correct path. Still: you'll have to choose which path to proceed on & you'll bear the full responsibility of your choices.

This continuously trains your decision-making muscles.
‼️Now, by no means is this to read that these skills are unique to people doing a PhD. These are life-long skills that various people nurture in various ways & to various degrees.

Doing a PhD is not at all necessary to gain such skills. But,in many instances,it can be sufficient
#AcademicTwitter is wonderful about sharing #PhDstudent advices.

Here however,I'm not offering advice on whether to do a PhD or not. It's your own journey & a personal decision to take.

Rather, I am highlighting PhD reasoning & mindset skills that are not sadly discussed enough
Informing yourself about:

1. The scientific topic of your PhD & its impact
2. The broad implications in terms of skill development of your PhD journey

will only help you decide better.

Most important is though: there's no correct decision!

Happy Halloween y'all 🎃

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More from @simocristea

Oct 31
New: the monthly roller-coaster through October’s coolest life science papers is here 🚀🧬

3-sentence summaries of papers on evolution, single cell methodologies, genetic screens & more.

And, only for October, an educational video on fighting cancer🤺 as a bonus.

Enjoy 3x10! Image
1. Assembly theory (Sharma et al., Nature)

The most (in)famous paper I read this month proposes a new framework (assembly theory, that is) to explain basically everything… or, more specifically, “to unify descriptions of evolutionary selection across physics and biology” 1/3 Image
This paper is not an easy read for anybody (in particular evolutionary biologists), but, to its merit, it sparked scientific discussions by being different than what is expected for a scientific paper describing evolution. 2/3
Read 38 tweets
Sep 22
The human genome is gradually unravelling its secrets 🎁

AlphaMissense model @ScienceMagazine: one more path lit up by deep learning in exploring the code of life 🧬

We now know with high confidence if 89% of ALL missense variants are benign or pathogenic

Key contributions🧵🧵 Image
First things first:

Missense variants = genetic variants (i.e DNA bases) that change the amino acid sequence (i.e groups of 3 bases, building blocks of proteins) in proteins.

Missense variants are more important than non-missense ones, as more likely to have functional impact. Image
Now, even if a variant changes the amino acid structure of a protein (i.e it is missense), it is not necessarily that the variant also impacts the function of its corresponding protein.

Further, even if protein function gets impacted, it isn't clear in which way or by how much.
Read 41 tweets
Jul 21
3 amazing papers just out @Nature, the kind worth giving up sleep for🦉

Spatial multi-omics human maps:
-placenta: MIBI & DSP
-intestine: CODEX & snRNAseq & snATACseq
-kidney: Visium & scRNA & scATAC

After sequencing single cells, we are now finally putting them back together🧵 Image
1. Placenta 1/5

Understanding the mysterious maternal processes that sustain embryo development is fascinating.

Mapping those spatially with proteins & mRNA to describe the maternal-fetal interface in the first half of pregnancy is really mind-blowing.…
1. Placenta 2/5

- 500,000 cells with MIBI of 37 antibody panel
- 66 individuals (6-20 weeks gestation)

Immune tolerance model proposed for how the structure & function of the maternal endometrium transforms to promote the regulated invasion of genetically dissimilar fetal cells Image
Read 19 tweets
Jun 20
Twitter messed up my previous thread, but this is too important to let it slide:

Here are (again) my summary & thoughts on early detection & an amazing work

Deep learning model trained on 9 million patient records in Denmark & US finds people at risk for pancreatic cancer
🧵🧵 Image
In this thread, we'll discuss:

1. Context & significance of study
2. Datasets
3. Deep learning model
4. Model performance
5. Feature interpretability
6. Thoughts

And here's the link to the paper:…
1. Context & Significance of Study

Pancreatic cancer is a terrible disease.

Despite impressive progress, its 5-year survival rate in the US is currently no more than 12%. Image
Read 56 tweets
Jun 1
Cancer is a terrible disease, and also one that we all know too well.

It is not a new problem, rather one that exists since thousands of years & is studied in unimaginable detail.

Then why do people still die of cancer?

Let's start understanding this by taking a step back. Image
It’s 1938, and Public Health Services are advising people that detecting and treating cancers early will save their lives. Image
Now fast-forward nowadays. We hear the exact same core message from the Public Health Services of our times, gradually and consistently backed up by more and more data. Image
Read 46 tweets
May 5
New preprint on scGPT: first foundation large language model for single cell biology, pretrained on 10 million cells.

Just as text is made of words, cells are characterized by genes

Some thoughts on how cool this is & why it challenges the status quo of single cell analysis🧵🧵 Image
The self-attention transformer (chatGPT) is so successful in natural language processing (NLP)

But maybe single cell biology is not that different from NLP, as genes & cells correspond to words & sentences?

That's the framing of @BoWang87's awesome paper…
Another core similarity between NLP & single cell biology is the large and ever-growing size of publicly available #scRNAseq data (e.g human cell atlas) to be used for training.

Can NLP models also understand intrinsic logics of single cell biology & develop "emergent thinking"?
Read 37 tweets

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