Bioinformatician. Interested in gene regulation, transcription factors, and data visualization. ᛃ
Joined August 2014
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Jaime A Castro-Mondragón retweeted
🧬Motifs are the new BLAST
Folddisco scans 53M AlphaFold structures for catalytic, binding or allosteric patterns in seconds🔎
18× quicker, 3.5× smaller, hits in seconds🌌
Jaime A Castro-Mondragón retweeted
Two new sequencing efforts shed light on Latin American genetic variation. Congrats to @hunemeier_t, @LygiaVPereira and their Brazilian team, and the #GenomeAsia100K team from @NTUsg. Science journalist @rpocisv wrote a nice piece on the DNAdoBrasil paper: science.org/content/article/…
Jaime A Castro-Mondragón retweeted
Check out our latest preprint, led by @schen_sc, that brings together an amazing team of scientists from several labs to tackle a fundamental problem in biology: how do cells regulate expression of their tRNAs? biorxiv.org/content/10.1101/…
Jaime A Castro-Mondragón retweeted
It was great taking part in writing this perspective on the cis-regulatory code with such excellent scientists.
@iscb @ISCB_RegSys has provided us an outstanding platform to share and discuss these topics over the years. Let's keep up the great work in this fantastic community.
Delighted to have worked on this perspective on the cis-regulatory code with @JuliaZeitlinger, @JasonErnstLab, @ferhatay, @AMathelier, @AleMedinaRivera, @mahonylab, @sinhasaur arxiv.org/abs/2411.04363. We provide an overview of current progress and some challenges to think about.
Jaime A Castro-Mondragón retweeted
Free scientific illustrations for biologists! 😍
@NIH has released a library of 500+ free scientific illustrations to create figures, presentations, and illustrations!
all freely available in the public domain.
Retweet and spread the message!
bioart.niaid.nih.gov/
Jaime A Castro-Mondragón retweeted
🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices.
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
doi.org/10.1093/bioinformati…
Jaime A Castro-Mondragón retweeted
Congratulations to @IevaRau for an outstanding PhD defense today!
Such fantastic work covered during the last 4 years with driving the last 2 releases of JASPAR @jaspar_db and the development of COBIND to predict TF co-binding.
I'm a very proud PI.
@NCMMnews @biovitenskap
Jaime A Castro-Mondragón retweeted
🎉 Excited to share the peer-reviewed version of our manuscript describing COBIND, a tool for revealing TF co-binding patterns using non-negative matrix factorization. Great work led by @IevaRau @NCMMnews @NordicEMBL @UniOslo_MED @UniOslo
academic.oup.com/nar/advance…
@NAR_Open
Jaime A Castro-Mondragón retweeted
We are very happy to announce that a dual new release of intOGen (intogen.org) and boostDM (intogen.org/boostdm/) is out today! 🎉 Here is a thread summarizing the main updates:👇
Jaime A Castro-Mondragón retweeted
How do enhancers work over distances that sometimes exceed megabases? Excited to share our work led by @gracecbower where we uncover a unique sequence signature globally associated with long-range enhancer-promoter interactions in developing limb buds: biorxiv.org/content/10.1101/… 1/
Jaime A Castro-Mondragón retweeted
Les compartimos este artículo de nuestro investigador, el Dr. @DavidRomeroC60 ,sobre un nuevo organelo celular cuya función es la de fijar nitrógeno: el nitroblasto.
"Nitroplastos y diazoplastos, los nuevos organelos que surgieron de las aguas".
acmor.org/publicaciones/nitr…
Jaime A Castro-Mondragón retweeted
You have perturbed TFs (for example disease vs healthy) and genome-wide H3K27ac data, what TF activity tools would infer the perturbed TFs that are more likely to be validated?
According to our results, the top 3 tools: RcisTarget, MEIRLOP and monaLisa
biorxiv.org/content/10.1101/…
Jaime A Castro-Mondragón retweeted
(1/14) Excited to share our new work on ZNF143/ZFP143 by @DomenicNarducci
ZNF143 has been widely reported to be a general loop factor
Instead we and @deWitLab in a companion preprint show that ZNF143 is a TF with no loop function:
biorxiv.org/content/10.1101/…
biorxiv.org/content/10.1101/…
Jaime A Castro-Mondragón retweeted
Join the IBIS Challenge: an open competition focused on the computational prediction of transcription factor binding motifs. IBIS aims to advance state-of-the-art methods for Inferring Binding Specificities of human transcription factors from diverse experimental data. (1/12)
Jaime A Castro-Mondragón retweeted
Great PhD defense from Rafael today! I'm a proud PI!
And thanks to the committee members @CarlMHerrmann @a_bardet for a fantastic discussion and @eviledv for the committee coordination.
Congratulations Dr Riudavets Puig 🎉🎉
Jaime A Castro-Mondragón retweeted
📣A second edition of our Introduction to #DataScience is on its way, now split into two books.
After teaching the course this semester, we've made significant improvements. Current drafts are online:
📘Intro: rafalab.dfci.harvard.edu/dsb…
📙Advanced: rafalab.dfci.harvard.edu/dsb…
#rstats
Jaime A Castro-Mondragón retweeted
Excited to share our latest findings on Oxygen Minimum Zones. Our study in Devil’s Hole, Bermuda, sheds light on the microbial response to reoxygenation in suboxic waters. #MicrobialEcology @BIOSstation
Suboxic DOM is bioavailable to surface prokaryotes in a simulated overturn of an oxygen minimum zone, Devil’s Hole, Bermuda frontiersin.org/articles/10.…
Jaime A Castro-Mondragón retweeted
Xmas present for UCSC users, an R package to easily build Track Hubs.
github.com/Novartis/easyTrac…
ps. is there any scientist left in this social network? where is everyone now?
Jaime A Castro-Mondragón retweeted
The long-awaited update of HOCOMOCO, the database of transcription factor binding motifs, received a major update after 5 years of efforts, see hocomoco12.autosome.org/
and doi.org/10.1093/nar/gkad1077
/cc @halfacrocodile @ZinkevichA (1/15)
