Simon Toftholm Jakobsens

PhD Fellow in the Siersbæk lab at @GenomicsUnit @NATsdu. Studying transcriptional regulation in cancers.

[Ming "Tommy" Tang @tangming2005]

8 Resources to study Transcription factor binding, enhancers and histone modification distribution
 1. ENCODE https://t.co/N5hScyoAoP

[Ming "Tommy" Tang @tangming2005]

1/ You tested 10,000 genes.
500 are significant (p < 0.05).
Exciting? Maybe.
But if you used raw p-values, you just got played by randomness.
Let’s talk FDR.

[Ming "Tommy" Tang @tangming2005]

Too many bioinformatics tools, too little time. Stop endlessly bookmarking—just pick one and start analyzing! 🧵👇

[Simon Toftholm Jakobsens @SimonToftholm]

Excited to share our new review on MYC in @oncogenejournal!🧬
We propose a model showing how MYC enhancer activity drives context-specific gene programs, distinct from core MYC target genes driven by E-box binding at promoters. Read more: https://t.co/RLEAmFSmA5 @RSiersbaek #MYC

[The Thought Emporium 🌻 @EmporiumThought]

We joke that DMEM is fancy Gatorade.... So how much DMEM can you replace with Gatorade before cells die? Lets find out!

[Angelos Georgakis @angelosgeo]

"Biologists and scientists are an angry crowd.", said Nvidia's Jensen Huang at the @RecursionPharma JPM24 event.

That's also my experience working with you guys. You're VERY angry, and that's the most beautiful thing about you.

I'll explain, but first, here's what Jensen said:

"I'm super excited to be here. First of all, this is not my normal crowd. Biologists and scientists are an angry crowd. When we think about things, we think about creation, we like to improve and accelerate, but you guys use words like target, inhibit, and words that are generally angry (angelos: my favourite is knockdown 😛). My normal crowd is creators, designers, artists, people who are generally happier! You guys are just in it so much. You're angry people with other angry people. Before you know it, you don't even realise you're angry. You're doing it for a good cause but yeah, you're doing it in a really angry way."

Anger and all the shades of it (frustration, irritability, annoyance) come up a lot in my work with you guys.

Here's a common one: "I don't want my team to see me angry and frustrated. I want to show up calm and collected."

When I hear that, depending on the situation, I say things like, "Your anger is the MOST beautiful thing to me. I feel safe with the angry leader you are. I knew you were the right person for this job. I'm as angry as you. My blood pressure goes up during every coaching call. Thank God you're angry; I'd be worried if you were not."

And you guys look at me confused.

Let me explain...

Your anger, biotech folks, shows how much you care. It shows how much you care about the company, the vision, and the patients.

You're angry because the stakes are high. You're running at full blast. There's urgency in what you do. There are lives to be saved. There is impact to be made.

You are Type-A freaks. You expect a lot from yourself, you expect a lot from your people.

And there's also survival! You are not pharma. Every day is a live-or-die for you.

Underneath your anger, there's often fear. Innocent, natural, legitimate human fear.

And under the fear, there are always good intentions, an existential anxiety to do good and succeed for the patients and everyone else who's with you on this journey.

There may be a burning desire for personal success too, and glory, and money, and respect from the community. At the very core, probably there is a human need to be loved. That's all okay. Welcome it all. Welcome...

Anger is the most misunderstood emotion. It can be tricky to understand it, but when you learn to deal with it properly, it can be powerful! There's a lot of energy in anger, and you can move from entropy to empowerment!

The key idea is this: The more you don't want to show your anger, the more you'll fall flat on your face.

Not wanting to feel the anger and suppressing it is like fighting yourself and that creates more anger. And not only that, but you also fail to learn from it, you fail to transform its energy into action and productivity, both for yourself and the team.

But how will the team respond? How am I going to be perceived? What if my anger impacts my team negatively?

Here's the trick... When you allow yourself to feel angry and everyone in the team to FULLY see your anger, a mysterious thing happens: you don't feel as angry anymore. What creates more anger is you fighting your anger. Remember that the first person who judges yourself for your anger is you.

And, seriously, do you think you can hide your anger? You just can't. Your team can see you. And when you're trying too hard to hide your anger, you create even more anxiety in your team. It's not what you feel that creates the problem, but the dissonance between what you feel and what you project to the outside.

What would happen to your anger, if you said, "I don't care if they see me angry." That's surrendering. Self-acceptance. Forgiveness. And before you realise it, you're not angry anymore. You are the person you always wanted to be, i.e. "the calm and collected". And you achieved that by accepting your not calm and collected self! Counterintuitive I know... just like science most of the time!

What else do I tell you? Okay, here's what the legendary basketball coach Phil Jackson has written about anger:

"Anger focuses the mind. It's an advance-warning system alerting us to threats to our well-being. When viewed this way, anger can be a powerful force for bringing about positive change. But it takes practice—and no small amount of courage—to be present with such uncomfortable feelings and yet not be swept away by them. My practice when anger arises is to sit with it in meditation. I simply observe it come and go, come and go. Slowly, incrementally, over time I've learned that if I can stay with the anger, which often manifests itself as anxiety, and resist my conditioned response to suppress it, the intensity of the feeling dissipates and I'm able to hear the wisdom it has to impart. Sitting with your anger doesn't mean being passive. It means becoming more conscious and intimate with your inner experience so that you can act more mindfully and compassionately than is possible in the heat of the moment."

By embracing the anger and allowing yourself to express it, you end up expressing it less...

Talking with a coach, mentor, or someone you can trust can help. Journaling helps. I go for a walk checking in with myself, "What are you feeling, Angelos? What's going on inside?" And I welcome it all.

Somatic techniques help too, i.e., "Where are you feeling the anger/frustration in your body?" I personally feel my anger in my temples in my head and a specific point on the left side of my chest. I use mantras like the one above, "Welcome, welcome, welcome" or "Breathe in the anger, breathe in the frustration, breathe in the fear."

I said to an angry CEO yesterday, "Biotech is the most spiritual business. There is no better place to practice emotional resilience, self-awareness, enlightenment, and all in between than biotech..."

All for now.

Loving you angry crowd, Angelos.

ps: A big thank you to my friend @drrichjlaw for bringing up what Jensen said at JPM. One extra resource for me to send to my beloved angry people. What a delight! Btw is it cycling how you deal with your anger, Rich? 😛

[Simon Toftholm Jakobsens @SimonToftholm]

https://t.co/WXVzxDUrOR

[Simon Toftholm Jakobsens @SimonToftholm]

So exited to share my first paper is now online @NatureGenet 🎉 If you are interested in MYC and transcriptional regulation in driving cancer development check it out 👇

[Rasmus Siersbæk @RSiersbaek]

Sooooo excited to share the first paper from the lab now online @NatureGenet 😀😀😀
Interested in MYC, transcriptional mechanisms and (breast) cancer? Check it out👉https://t.co/3FU5B2RNcO.
Short summary thread 👇

[Cohesin @Xieeee4]

🍺I am so excited that my first paper is online (https://t.co/gwg6bc6l62)! Joint profiling of histone modifications and transcriptome are critical to understand the active or repressive gene regulatory network. We therefore develop Droplet Paired-Tag,

[Niko McCarty. @NikoMcCarty]

There have been an incredible number of gene-editing advances (including in delivery) over the last three days.

Here are 7 of them...🧵

[antisense. @razoralign]

xcore: an R package for inference of gene expression regulators https://t.co/RXOXxepqas

[Simon Toftholm Jakobsens @SimonToftholm]

Happy to share the pre-print of my P.hD. work on the transcriptional role of MYC in activating cancer type-specific enhancers! 🥳
https://t.co/Pa4etf7zeD

[Rasmus Siersbæk @RSiersbaek]

📢Super excited that the first pre-print from the lab on the role of MYC enhancer invasion in cancer is now online https://t.co/VrJM1woklR🥳 #MYC #CancerResearch #breastcancer
Can't think of a better way to start the new year @GenomicsUnit @bmbSDU @NATsdu!

[Fabian Theis @fabian_theis]

1/n Single-cell data analysis is complex with many tools to choose from - but which ones work best and should be used when? Led by @lukasheumos and @AnnaCSchaar, we wrote a free online book that aims to guide single-cell data analysts: https://t.co/UMU5c7S6pF

[Xi Chen @XiChenUoM]

I somehow missed it when first came out, only got to know this after the revised ver. now. This is wild. Seems like inDrop but in the tube w/o the device.

“Regardless the tube size, only two minutes of vortexing is required for cell capture.” - very nice https://t.co/VhbtGlLAi3

[Simon Toftholm Jakobsens @SimonToftholm]

@PhD_Genie @LasseLehtonenDK det er da en meget præcis beskrivelse? 😃

[Simon Toftholm Jakobsens @SimonToftholm]

@tangming2005 @IsabellVSE

[Simon Toftholm Jakobsens @SimonToftholm]

Inspiring and fun week at the #EMBO 20/20 vision of the future of #NuclearReceptor together with the Siersbæk lab!

[antisense. @razoralign]

ggcoverage: an R package to visualize and annotate genome coverage for various NGS data https://t.co/2m7gjRSOhI

[Bernardo Almeida @deAlmeida_BP]

What are the rules of enhancer syntax? How flexible/constrained TF motif positions within enhancers are? How does the sequence context modulate the contribution of motifs to enhancer function?

Excited to share our work together with @reiterfanny addressing these questions!

1/19

[Rasmus Siersbæk @RSiersbaek]

Today was a fantastic day in the lab as @SimonToftholm defended his PhD thesis @GenomicsUnit @bmbSDU @NATsdu! He was an absolute star😃 amazing job, Simon! Many thanks to @zwartlab @Bo_Porse @Grontved_Group for a great scientific discussion.