Carlos Guzman

he/him. Gene expression, epigenetics and non-coding transcription regulation nerd. bioinformatics phd.

[Anshul Kundaje @anshulkundaje]

There is a reason I have consciously stayed clear of training and using large AI models in biology before understanding precisely how & what smaller incarnations learn. Here is the fundamental problem 1/

[Zihan Xu @xu_zxu]

Nice to see ultra-short term EU labeling applied for #singlecell RNA dynamics, revealing intergenic transcription.
With 1h labeling coupled to ATAC and #CRISPR perturbations, we traced gene-regulatory dynamics during cell state transitions. Check out scFluent-seq and PerturbFate!

[Carlos Guzman @enhancer_RNA]

@iannuttall @aipreneur_j Did they ever implement screen/tmux comparability? … last I tried I couldn’t tmux into new sessions which made it a bit useless for my workflow

[Carlos Guzman @enhancer_RNA]

@yacineMTB Use pixi

[Ian Nuttall @iannuttall]

OMG somebody built a Tamagotchi pet that lives in the Claude Code status and reacts to your coding sessions 😍

(Link below)

[Carlos Guzman @enhancer_RNA]

@anshulkundaje @pkoo562 Thanks! Makes sense!

[Cell Genomics @CellGenomics]

Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex https://t.co/06YRl3sKjw

[Juhyun Kim @juhyunk_]

Rewriting regulatory DNA to dissect and reprogram gene expression https://t.co/DYJT7V6mmL #journals #feedly

[Carlos Guzman @enhancer_RNA]

@EkStasevich Great thesis topic! I’m not biased at all! :)

[Dr. Kaia Mattioli @kaia_mattioli]

our work on the molecular differences between transcription factor isoforms is out now in @MolecularCell!

key point: 2/3rds of TF isos differ in important properties like DNA binding & transcriptional activity

many are "negative regulators" that are misexpressed in cancer

[jackson hoffman @jx_hoffman]

I'm super happy to now be able to share the published version of our paper at @ScienceAdvances showing that:
1) active histone mods occur independently of transcription
2) transcription coordinates histone deacetylation at active promoters
https://t.co/UOcOHN1k7A

[Peter Koo @pkoo562]

[SAVE THE DATE] MLCB 2025 is happening Sep 10-11 at the NY Genome Center—NYC!

Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections!

Submission deadline: Jun 1
Details: https://t.co/yI9YZV676c

Spread the word—please RT!

[Molecular Cell @MolecularCell]

Enhancer cooperativity can compensate for loss of activity over large genomic distances https://t.co/0LbAYI4fUL

[Carlos Guzman @enhancer_RNA]

@strnr @nf_core Chromap indexes would be a good addition!

[Taekjip Ha @taekjip]

Reliable amplification of highly repetitive or low complexity sequence DNA enabled by superhelicase-mediated isothermal amplification https://t.co/B0JUauiGQK

[Anshul Kundaje @anshulkundaje]

Brilliant hard work to create a benchmarking framework to show convincingly that the whole field of gene expression forecasting (perturbation predictions) has deep problems (as shown by several other recent benchmarks), especially the fancy single cell foundation models. 1/

[David Garfield (@[email protected] and post) @dagarfield]

A great collaboration with the ML team here at Genentech. Happy to see this pre-print out: https://t.co/QTpIkcLE5H (@lal_avantika @gokcen @suragnair and many others)

[Krishna Shrinivas @shrinivaslab]

Excited for 1st paper from our lab - led by the amazing @RyanKrue in collab. with @BrennerGroup1.

How do we design intrinsically disordered proteins (IDPs) that lack a stable structure and are continuously shapeshifting for different target functions?

https://t.co/OjIpmOGyZ1

[Prof. Nikolai Slavov @slavov_n]

An excellent introduction (for beginners) to Graph Neural Networks

https://t.co/q4MiMAjbWX