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footprintDB - a database of transcription factors with annotated cis elements (DNA motifs and sites) and binding interfaces

Reposted by Bruno Contreras Moreira

Jóvenes para la cooperación @cooperacion.bsky.social · Jul 25

🏫📚 Los días 25 y 26 de septiembre de 2025 el paraninfo de la Universidad de Zaragoza acogerá la IV Edición del curso sobre la Carrera Investigadora.

@unisevilla.bsky.social

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Bruno Contreras Moreira @brunocontrerasm.bsky.social · Aug 19

Our footprintdb.eead.csic.es server has been updated, marking the 19082025 release: bioinfoperl.blogspot.com/2025/08/foot...

footprintDB Database

footprintdb.eead.csic.es

Deconvolution of Single Homeologous Polymorphism (SHP) drives phylogenetic analysis of allopolyploids

Reposted by Bruno Contreras Moreira

Mary Williams @PlantTeaching @plantteaching.bsky.social · Jul 30

Before this #PlantBio2025 thread closes: two exciting opportunities now open for early-career plant scientists.
1. Plantae Fellows program, apply by Aug 31 plantae.org/2026fellowsa...
2. @theplantcell.bsky.social Assistant Features Editor program, apply by Sep 15.
blog.aspb.org/the-plant-ce...

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Bruno Contreras Moreira @brunocontrerasm.bsky.social · Jul 28

@biorxivpreprint.bsky.social from Rubén Sancho describes phylogenies of allopolyploids out of sequence reads and the genomes of related diploid genomes. Part of PhD work, now tested on Brachypodium, Brassica, Triticum and also yeasts:
www.biorxiv.org/content/10.1...

lnkd.in/dU-Eqmfy

The genomic and evolutionary study of allopolyploid organisms involves multiple copies of homeologous chromosomes, making their assembly, annotation, and phylogenetic analysis challenging. Bioinformat...

www.biorxiv.org

Bruno Contreras Moreira @brunocontrerasm.bsky.social · Jul 24

Check out a reproducible protocol for ddRAD-seq + GWAS benchmarked by Najla Ksouri doi.org/10.1186/s130...

Tested on peach varieties but should work on other diploid species.

Code and documentation at github.com/najlaksouri/...

PS read more In Spanish at bioinfoperl.blogspot.com/2025/07/prot...

A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach - Plant Methods

Improving peach cultivars with superior traits is a primary objective of breeding initiatives. In this study, we aimed to elucidate the genetic basis of key agronomic and fruit-related traits using a ...

doi.org

Protocolo reproducible de ddRAD-seq + GWAS

Bruno Contreras Moreira @brunocontrerasm.bsky.social · Jul 23

Comparto el protocolo de ddRAD-seq + GWAS de Najla Ksouri:

bioinfoperl.blogspot.com/2025/07/prot...

bioinfoperl.blogspot.com/2025/07/line...

Bruno Contreras Moreira @brunocontrerasm.bsky.social · Jul 16

líneas distintas entre ficheros con grep

Are groundbreaking science discoveries becoming harder to find?

Reposted by Bruno Contreras Moreira

International Barley Hub @intbarleyhub.bsky.social · Jun 9

IBH Seminar Announcement‼️
📜 Advances in Understanding Crown Root Formation in Barley
🔊 Nikola Kořínková. Czech Advanced Technology and Research Institute
📆 Thursday 12th June 14.00 BST
🔌 hutton.webex.com/weblink/regi...

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Bruno Contreras Moreira @brunocontrerasm.bsky.social · Jun 3

Added BarT2 and panBaRT genes to facilitate cross-analysis at EoRNA and panBaRT at barleymap.eead.csic.es #barleymap

Barleymap

barleymap.eead.csic.es

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Bruno Contreras Moreira @brunocontrerasm.bsky.social · May 28

No había oído hablar del CD index: www.nature.com/articles/d41...

Researchers are arguing over whether ‘disruptive’ or ‘novel’ science is waning – and how to remedy the problem.

www.nature.com

Bruno Contreras Moreira @brunocontrerasm.bsky.social · May 15

Aprende a descarga datasets del NCBI desde el terminal en bioinfoperl.blogspot.com/2025/05/desc...

Bruno Contreras Moreira @brunocontrerasm.bsky.social · May 6

Check out the latest preprint from Chesco Montardit's thesis at EEAD-CSIC

www.biorxiv.org/content/10.1...

Vernalization regulatory network identifies potential novel functions for ZCCT genes within HvVRN2

### Competing Interest Statement The authors have declared no competing interest. Agencia Estatal de Investigación, https://ror.org/003x0zc53, AGL2016-80967-R, PID2019 111621RB I00, PID2022 142116OB...

www.biorxiv.org

Bruno Contreras Moreira @brunocontrerasm.bsky.social · May 5

Thank you, Alfonso: An Impactful Bioinformatics Collection: academic.oup.com/bioinformati...

Thank you, Alfonso: An Impactful Bioinformatics Collection

Last year marked 20 years of Alfonso leading Bioinformatics. We are expressing our gratitude and celebrating his remarkable contributions by highlighting some o

academic.oup.com

Bruno Contreras Moreira @brunocontrerasm.bsky.social · Apr 30

Thanks so much for the invite, had a great day, the campus was beautiful and the meetings quite fun!

bioinfoperl.blogspot.com/2025/04/uso-...

Bruno Contreras Moreira @brunocontrerasm.bsky.social · Apr 29

Uso aceptable de modelos de lenguaje según la ISCB

bioinfoperl.blogspot.com/2025/03/asam...

Reposted by Bruno Contreras Moreira

BCBHubCSIC @bcbhubcsic.bsky.social · Mar 19

📌Abierto el plazo de solicitudes de candidatos a las becas JAE INTRO ICU 2025 ofertadas por @bcbhubcsic.bsky.social Tienes toda la información sobre la convocatoria, planes formativos en 👉 conexion-bcb.csic.es/convocatoria... y en la sede electrónica del CSIC sede.csic.gob.es/tramites/pro....

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Bruno Contreras Moreira @brunocontrerasm.bsky.social · Mar 14

Ten simple rules for a mom-friendly Academia

Reposted by Bruno Contreras Moreira

Protein Data Bank in Europe (PDBe) @pdbeurope.bsky.social · Mar 12

🚀 Exciting Opportunity 🚀
Do you have a passion for structural biology?

We're hiring at @PDBeurope! 🌟

Apply now to help annotate biological data 💻 🔬
🔗 embl.wd103.myworkdayjobs.com/en-US/EMBL/d...

Closing date: April 6, 2025

#JobOpening #StructuralBiology #Bioinformatics #ScienceJobs #Hiring

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Bruno Contreras Moreira @brunocontrerasm.bsky.social · Mar 10

Ten simple rules for a mom-friendly Academia
doi.org/10.1371/jour...

Author summary Although there is an increasing awareness of the importance of having more diverse scientific communities, the number of women in science is still low. A large proportion of the women w...

doi.org

Reposted by Bruno Contreras Moreira

Adriana Guatame-García @adrianaguatame.bsky.social · Mar 6

A friend included this anti-acknowledgement section on her PhD thesis. She also added the proposition: “Systematic bullying and undermining of girls and women in STEM starts early on and is the reason why they do not stay in science and related fields.”
Absurd we still need to go through this
🧪👩‍🔬

There have been people less than helpful in my journey here. I wanted to acknowledge those too, bc I know I am not unique in this experience.
No thank you to the physics study assoc that made me sing songs about how women couldn't study physics without sleeping with the professor, the day I stepped into university life. No thank you to the 5th year physics student that decided to assign me a stripper name within the first minute of meeting me in the physics coffee corner in my first year. No thank you to the technician that was responsible for onboarding me on the use of the cluster in my third year who raised his eyebrows and asked me if that meant I was some sort of computer girl. No thank you to the senior researcher that sent me utterly inappropriate texts after a conference, then proceeded to apologise months later by telling me they had not been meant for me anyway so no hard feelings remain hopefully And no thank you to him for attending every conference I've been to since. No thank you to the people who told me that it was surprising that I was doing a PhD since I was a girl. No thank you to the man who mistook me for a coffee lady at a conference, and after having to correct him two times that I did not work there, responded with you should consider it. No thank you to the researcher that asked me what I was wearing underneath my outfit during a conference. No thank you to the physicist who declared to a room full of other physicists that biologists don't know how to design an experiment. No thank you to the people who have called me scary instead of strong and intimidating instead of intelligent.
And finally, no thank you to the exec board of the TU Delft, whose knee-jerk reaction to being held up a mirror about the social safety at the university, was to sue the party holding up the mirror instead of looking at the problems they highlighted.
... You have made me feel like I do not belong in science & I cannot forgive you for that.

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Bruno Contreras Moreira @brunocontrerasm.bsky.social · Feb 27

bioinfoperl.blogspot.com/2025/02/pyth...

Python tool to plot genomic data

A pan-gene catalogue of Asian cultivated rice

Bruno Contreras Moreira @brunocontrerasm.bsky.social · Feb 27

In case you haven't checked out the latest preprint from the #PanOryza consortium: www.biorxiv.org/content/10.1...

@biorxivpreprint.bsky.social

The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Populat...

www.biorxiv.org