PhD in systems biology @Harvard @KleinLabHMS. Ex digital nomad @MinervaUni @sfiscience. Genomics immunology machine learning. Jazz 𝄢. 🇦🇷🇧🇷🤟
Joined April 2009
- Tweets 822
- Following 456
- Followers 486
- Likes 2,549
59 Photos and videos
20 Aug 2024
Welcome!
19 Aug 2024
Some exciting news to share! Our lab is relocating to @harvardmed Systems Biology and @BrighamWomens GI & Genetics this fall. We're actively recruiting talented postdocs to join our team. Please RT to spread the word.
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4 Jun 2024
This account endorses NICH as a valid pronunciation of niche.
3 Jun 2024
I seem to have started a war in the comments. Americans pls get off my BACK, you’re all wrong. Own your mess
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10 May 2024
The most important unexpected lesson of my PhD.
9 May 2024
There’s a second layer I had to learn (and find other quant-turned-biologists I teach struggle with) which is to not overthink before trying something—that there are so many unexpected twists you hit the limit of what you can plan by thinking much earlier than you expect
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Nico Gort-Freitas retweeted
16 Feb 2024
Our 🪐SATURN method is now out in @naturemethods!
SATURN paves the way for universal cell embeddings, enabling integration of datasets across different species 🐒🐁🧍🐟🐸 Using protein language models, we encode biological meaning of genes in scRNA-seq datasets.
16 Feb 2024
SATURN performs cross-species integration and analysis using both single-cell gene expression and protein representations generated by protein language models. @jure @YanayRosen @mariabrbic @yusufroohani
nature.com/articles/s41592-0…
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Nico Gort-Freitas retweeted
6 Oct 2023
"These methods can order a set of individual cells along a path, and assign a pseudotime value to each cell that represents where the cell is along that path. This can be a starting point for further analysis to determine gene expression programs driving cell phenotypes."
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16 Aug 2023
Another outstanding study by Mikaël's group! @RubenBill5 et al. disentangled key axes of variation in the TME and their influence on cancer prognosis, showing that CXCL9:SPP1 polarization in macrophages is more predictive of patient survival than M1:M2 🤯.
7 Aug 2023
📢 Research Alert! 🧬🔬 🩺 We are super excited that our latest study, led by the great @RubenBill5 & Asa Wirapati, is out: science.org/doi/full/10.1126…
We set out to shed some light on the tumor microenvironment and its impact on cancer progression.
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Nico Gort-Freitas retweeted
31 Jul 2023
🎉 Excited to share a big part of my PhD work in @KleinLabHMS that took many, many years and my blood, sweat, and tears! 😅
We ask - What’s the role of cell division in the formation of initial cell types during early development ?🧐
biorxiv.org/content/10.1101/…
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Nico Gort-Freitas retweeted
28 Jun 2023
This is the best video to introduce a computational biology course. There will never be a better one
x.com/fan_of_gpu/status/1673…
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Nico Gort-Freitas retweeted
2 May 2023
scRNA-seq is great for non-model organisms—with just a transcriptome you can discover new cell types. But for many marine organisms there's one big problem: SALT 🧂
A solution from our awesome student Tal Scully (1/7🧵)
biorxiv.org/content/10.1101/…
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1 May 2023
Congrats @MariusMessemak1!
1 May 2023
Excited to share STAPLER, a language model to predict TCR – pMHC reactivity that outperforms prior models.
And for ML aficionados: Description of a new data leakage problem inherent to a common negative data generation strategy.
biorxiv.org/content/10.1101/…
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Nico Gort-Freitas retweeted
16 Apr 2023
Ahmad Jamal was someone who always left me completely starstruck. I’ve stood in a room with him numerous times and never had the guts to say hello. His vibe was just too regal. Thank you, Mr. Jamal for all the music you gave us. 🙏🏾❤️ RIP.
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Nico Gort-Freitas retweeted
30 Mar 2023
Neutrophils — the most common cell type in the immune system — play a key role in immunotherapy success hvrd.me/vv3X50Nw2xn
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Nico Gort-Freitas retweeted
30 Mar 2023
Shout out to @Nich, @jgungabeesoon, @Mate_Kiss on our paper doi.org/10.1016/j.cell.2023.… on heterogeneity in tumor neutrophils and why it matters. A great summary by @PittetLab below:
30 Mar 2023
❔What is special about an immune system that successfully attacks tumors, compared to one that doesn’t?
Our new study in @CellCellPress led by @jgungabeesoon, @Nich and @Mate_Kiss_ aimed to address this question. A joint work with the great @KleinLabHMS
authors.elsevier.com/a/1gqie…
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30 Mar 2023
Thrilled to share our latest work elucidating the critical role of neutrophils in successful cancer immunotherapy, featured in @CellCellPress.
authors.elsevier.com/c/1gqie…
30 Mar 2023
❔What is special about an immune system that successfully attacks tumors, compared to one that doesn’t?
Our new study in @CellCellPress led by @jgungabeesoon, @Nich and @Mate_Kiss_ aimed to address this question. A joint work with the great @KleinLabHMS
authors.elsevier.com/a/1gqie…
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30 Mar 2023
Come learn about the business of biotech in our case study course led by HBS faculty and industry experts. All Harvard affiliates are invited to apply!
Are you interested in learning about biotechnology entrepreneurship? If so you should apply for the Crossover course! Crossover teaches trainees the HBS case study method and how to apply it to real-world scenarios centered around the biotechnology industry.
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8 Feb 2023
A very elegant approach to simulating cell state transitions based on inferring gene regulatory networks locally and then walking through the cell state manifold by propagating in silico TF perturbations. Excellent work by @kenjikamimoto68 and @morris_lab!
8 Feb 2023
At last! Happy to share our paper on CellOracle – a computational method for dissecting cell identity via network inference and in silico gene perturbation, led by the amazing @kenjikamimoto68: nature.com/articles/s41586-0…
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Nico Gort-Freitas retweeted
22 Sep 2022
It's time for the 2022 application cycle! We are reopening our @HMS_SysBio SSQBio application assistance program for the third year at the following link. Can't wait to meet the new applicants!
forms.gle/DyshN9KfbAznQVTF9
6 Oct 2020
Students in SSQBio @ Harvard want to make sure everyone has access to resources when applying to graduate school, so we created an application assistance program (AAP) and an email helpline to assist current applicants. Links below (1/3)
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Nico Gort-Freitas retweeted
6 Oct 2022
We’re thrilled to share MrVI, a deep generative model for analyzing sample-level heterogeneity in single-cell RNA-seq datasets! This work with @pierreboyeau and @adamgayoso @YosefLab was born out of a simple yet challenging question: what can we do with large-sample data? 1/
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21 Sep 2022
This is the best summary of my conversations with Sid while at @sfiscience.
I highly recommend his episode of the Complexity podcast (h/o @michaelgarfield) to hear about his approach to choosing interesting problems. Link: open.spotify.com/episode/1Tq….
Per past discussions of 'good taste in problems', Sid Redner's work is among my absolute favorites when it comes to taste in problems.
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