@Nich

PhD in systems biology @Harvard @KleinLabHMS. Ex digital nomad @MinervaUni @sfiscience. Genomics + immunology + machine learning. Jazz 𝄢. 🇦🇷🇧🇷🤟

 Cambridge, MA
Joined April 2009
  • Tweets826
  • Following477
  • Followers486
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Nico Gort-Freitas retweeted
Maria Brbic@mariabrbic16 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.
Nature Methods@naturemethods16 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
Lior Pachter@lpachter6 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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Nico Gort-Freitas retweeted
Kalki Kukreja@KalkiKukreja31 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/… 🧵 (1/14)

Global decoupling of cell differentiation from cell division in early embryo development

As tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of...

biorxiv.org
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Nico Gort-Freitas retweeted
Phillip Compeau@PhillipCompeau28 Jun 2023
This is the best video to introduce a computational biology course. There will never be a better one xitter.cf/fan_of_gpu/status/1673…
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Nico Gort-Freitas retweeted
Allon Klein Lab@KleinLabHMS2 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/…

A mannitol-based buffer improves single-cell RNA sequencing of high-salt marine cells

Single-cell RNA sequencing (scRNA-seq) enables discovery of novel cell states by transcriptomic profiling with minimal prior knowledge, making it useful for studying non-model organisms. For most...

biorxiv.org
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Nico Gort-Freitas retweeted
Christian McBride
@mcbridesworld16 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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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
Allon Klein Lab@KleinLabHMS30 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:
The Pittet Lab@PittetLab30 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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Nico Gort-Freitas retweeted
Ellie Rand@EllieRand322 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

2022 SSQBio Application Assistance Program (AAP) Registration

The Systems, Synthetic and Quantitative Biology (SSQBio) Application Assistance Program (AAP) is a volunteer-student run program meant to assist eligible applicants to the PhD program for the...

docs.google.com
Ellie Rand@EllieRand36 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
Justin Hong@justjhong6 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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Nico Gort-Freitas retweeted
Seth Shipman@seth_shipman27 Jul 2022
I’m excited to introduce our Retro-Cascorder, out today in @Nature! This molecular device logs barcoded receipts of gene expression in a temporal genomic ledger. Sequence the ledger --> recover the history of gene expression. nature.com/articles/s41586-0…
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Nico Gort-Freitas retweeted
Blood Cancer Discovery@BCD_AACR28 Jun 2022
#ICYMI - Rise of the Clones: Myelodysplastic Syndrome to Secondary #AcuteMyeloidLeukemia, by @vangalenlab and @KyleRomine12. bit.ly/3HYbhLI @BrighamResearch #MDSsm #AMLsm #leusm
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Nico Gort-Freitas retweeted
Haas Lab@haas_lab5 May 2022
Excited to share our most recent publication @CellStemCell. Unexpectedly, we found that hematopoietic stem cells act as antigen presenting cells! Antigen presentation safeguards the integrity of the stem cell pool and prevents the onset of leukemias (1/8).authors.elsevier.com/c/1f128…
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Nico Gort-Freitas retweeted
Joseph Powell@drjosephpowell7 Apr 2022
Our work “Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease” just published in @ScienceMagazine. The work started with the creation of the OneK1K cohort, consisting of scRNA-seq data on PBMCs from ~1000 donors science.org/doi/10.1126/scie… 🧵

Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease

Cell type and context affects gene expression affecting immune-mediated disease.

science.org
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Nico Gort-Freitas retweeted
Beth Psaila@beth_psaila17 Mar 2022
Need a human bone marrow system for mechanistic studies and target validation? Our bone marrow #organoids pre-print is out! biorxiv.org/cgi/content/shor… 1/5
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Nico Gort-Freitas retweeted
Allon Klein Lab@KleinLabHMS23 Feb 2022
I am really excited to share our latest work on inferring differentiation trajectories by incorporating transcriptome and lineage tracing information, now in @NatureBiotech. CoSpar performs really well in resolving early fate choices in lineage tracing data. Please try it out!
shouwen wang@ShouwenW23 Feb 2022
CoSpar with @KleinLabHMS is out at Nature Biotech! CoSpar robustly infers cell fate choice by integrating transcriptome and lineage tracing information. It reveals early fate bias across hematopoiesis, reprogramming, and directed differentiation. Link: rdcu.be/cHsqT
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Replying to @IdeTahiti @theosanderson
Dès que le R0 est > à 1, c’est une exponentielle. Cela commence bien avant de ressembler à une falaise, mais, pour la grande majorité d’entre nous, nous n’avons pas l’œil exercé pour le voir.
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Nico Gort-Freitas retweeted
Madeleine Baker@madeleineebaker2 Jan 2022
Among the many failings of the Jedi in the waning hours of the Republic, perhaps the most fateful was their invention of the dreaded "hybrid meeting format"
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Thanks to 100% vaccine coverage, universal PCR or rapid testing before each and every rehearsal, and a love for Mozart… Here’s a clip of me conducting @LongwoodChorus at our dress rehearsal. Yes, these performers are all members of Boston’s medical/science community. ❤️❤️❤️
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