Sergio Civera retweeted
Check out this fantastic final project by one of our former students, who did his internship with us as part of his Master’s in Bioinformatics. Congratulations @scivera ! From now on, I’ll be the one asking you for help.
1/3 There is no one-size-fits-all solution in #Bioinformatics.
Genome characteristics and research objectives can vary significantly between species, making it essential to develop flexible workflows tailored to the organism and the analysis being performed.
Sergio Civera retweeted
⏳🧬 ONLY 5 DAYS TO GO! Are you ready to explore the world of genomics with Ensembl? 🌍💻
The countdown is on! 🚀 Join the ISCB-SC × EMBL-EBI EduSearch Series with Ensembl for three days of online learning, featuring Jorge Batista da Rocha, Senior Ensembl Outreach Project Leader at EMBL-EBI.
🔬 Here’s what’s coming up:
📅 26 October: Introduction to Ensembl, Selecting Genomes and Genome Browsing
🧬 27 October: Gene Annotation, Exploring Genomic Features and Exporting Data
🧪 28 October: Using the Ensembl Variant Effect Predictor (VEP) to Annotate and Explore Variants
⏰ Time: 10:00 UTC daily
💻 Format: Online | 1 hour per day
📜 Certificates will be provided!
Whether you're a student, researcher, or aspiring bioinformatician, this is your chance to build practical skills and discover powerful tools for exploring genomic data.
🎯 Haven’t registered yet? Sign up now!
🔗 forms.gle/kdCytrAjnbLzpMPb9
📣 Tag a friend who should join you on this genomics journey!
#5DaysToGo #Ensembl #Bioinformatics #Genomics #ComputationalBiology #EMBLEBI #ISCBSC #EduSearch
@ISCB_RSG_India @RSG_nigeria @ensembl
Sergio Civera retweeted
💬 David Klenerman y Shankar Balasubramanian, Premio Princesa de Asturias de Investigación Científica y Técnica 2026 junto a Pascal Mayer, han compartido su labor sobre la secuenciación de ADN de nueva generación con estudiantes de las ramas biosanitarias de la Universidad de Oviedo. El encuentro, celebrado en la Facultad de Medicina, ha sido moderado por Víctor Quesada, profesor de Bioquímica y Biología Molecular.
© FPA | Julián Rus
#PremiosPrincesadeAsturias #PrincessofAsturiasAwards #InvestigaciónCientíficayTécnica #TechnicalandScientificResearch #DavidKlenerman #ShankarBalasubramanian
1/3 There is no one-size-fits-all solution in #Bioinformatics.
Genome characteristics and research objectives can vary significantly between species, making it essential to develop flexible workflows tailored to the organism and the analysis being performed.
2/3 With this in mind, for my Master's thesis in #Bioinformatics, I developed a genome assembly and repetitive element annotation workflow for plant genomes using #Snakemake.
It was a great opportunity to bring together my interests in #Genomics and transposable elements.
3/3 The workflow integrates PacBio HiFi and Hi-C data for genome assembly, quality assessment, chromosome-level scaffolding, and repetitive element annotation.
This is a project I hope to keep improving and expanding!
github.com/scivera10/tfm_bio…
Sergio Civera retweeted
Did you know you can calculate the exact sample size you need before you even start your study? A sample size calculation — also called a power analysis — helps you determine the optimal number of observations for your statistical analysis. It ensures your study is large enough to detect meaningful effects, but not so large that you waste resources.
Key advantages of performing a power analysis:
✔️ Avoid underpowered studies that might miss real effects
✔️ Save time and costs by avoiding unnecessarily large samples
✔️ Tailor your sample size to the effect size you care about detecting
✔️ Choose your desired confidence level and statistical power for robust results
✔️ Works for a wide range of statistical tests, from t‑tests to ANOVA and regression
✔️ Supported by many free R packages, such as pwr
The image shows on the left side how the required sample size changes depending on the expected effect size — smaller effects require much larger samples. On the right side, you see an example of a calculated sample size for comparing two groups using a t-test, showing exactly how many participants are needed per group for the desired confidence level and statistical power.
Sign up for my newsletter to get more practical tips on statistics, data science, R, and Python. More details are available at this link: statisticsglobe.com/newslett…
#database #DataAnalytics #Python #DataScience #statisticsclass #RStats
Sergio Civera retweeted
✝️ Así regresaba la Virgen de la Merced @Hdad_Merced a San Antonio de Padua con sones de @BMTubamirum
Sergio Civera retweeted
How do bacteria build their flagella?
We’ve put together an animation of Salmonella flagellum assembly based on cryo-EM and X-ray structures.
From the membrane-embedded machinery to the growing filament, here’s how the parts come together, step-by-step.
Claude now works inside Google Docs, Sheets, and Slides, and those files also open inside Claude.
In Google Workspace, Claude sits in a sidebar next to your file, reads what you have open, and edits it in place. You can approve each edit before it lands.
Sergio Civera retweeted
Out today in @nature.com: our review on how single cells evolve into multicellular organisms, with Ozan Bozdag, @kai_tong_mc25, Peter Yunker, and Matt Herron.
rdcu.be/9ZuiKow9twKa
For an overview, check out the video below.
I've just joined Bluesky! I’ll be sharing posts about #bioinformatics and #programming there as well.
You can find me as @scivera.bsky.social, looking forward to connecting with the community there too!
2/3 The idea came from a mathematical curiosity: π is irrational, so its decimal expansion never ends and never becomes periodic. That doesn’t mean we know that every possible pattern must appear in π, but searching for what does appear is a pretty fun experiment.
3/3 What I found interesting is that some of the same ideas show up in bioinformatics too: working with long sequences and looking for patterns in them.
I’ve uploaded the project to GitHub.
👇
github.com/scivera10/learnin…
#Python #Bioinformatics #Pi
1/3 I built a small “π Explorer” in Python: it generates 10 million digits of π, stores them, converts them into a sequence of letters, and lets me search for numeric or text patterns across millions of positions.
Quick demo below 👇
Sergio Civera retweeted
Two tools for plotting genomics data:
figeno: Tool for making genomics figures in #python.
github.com/CompEpigen/figeno
Plotting Multi-omic Data with plotgardener in #rstats
phanstiellab.github.io/plotg…
Sergio Civera retweeted
Retrotransposons can "hop" from a somatic cell into a germline cell, thus passing down to future generations.
Before, it was thought that retrotransposons (which are basically stretches of DNA that generate copies of themselves through RNA, which gets converted back into DNA and pasted into the genome) would solely hop around within a single cell's genome.
But it turns out that in flies, some retrotransposons encode a tiny protein called sORF2 that helps them get into another cell. The cells surrounding the egg encode these retrotransposons that get transcribed into RNA. Part of that RNA encodes sORF2, which the cell then makes. This protein forms some kind of interaction with the RNA, forming an extension or "protrusion" that pushes it into a neighboring cell, like the egg itself. The original retrotransposon DNA stays behind.
For this paper, they watched these particles move into the egg, which is crazy. And when they disabled sORF2, the protrusions stopped forming and the transfer stopped. These retrotransposons are basically a miniature form of virus. Biology continues to get weirder.
Sergio Civera retweeted
Visualize genomic data with ease using gggenomes, an R package that extends ggplot2 to handle and display genomic information intuitively. Whether you’re comparing genomes, analyzing features, or showcasing synteny, gggenomes provides the tools you need to turn complex genomic data into clear, informative visualizations.
Why use gggenomes?
✔️ Genomic-focused visualizations: Specifically designed for handling genomic data, including features, alignments, and comparative analysis.
✔️ Versatile and modular: Create detailed and layered plots for diverse genomic scenarios with flexibility for customization.
✔️ Built on ggplot2: Leverages ggplot2’s familiar framework, making it easy for users to adapt and enhance their visualizations.
The example visualization shown here is taken directly from the gggenomes GitHub repository, demonstrating how it transforms genomic data into compelling plots: github.com/thackl/gggenomes
Curious to learn more about creating data visualizations in R and using tools like ggplot2 and its extensions? Check out my online course, "Data Visualization in R Using ggplot2 & Friends!"
See this link for additional information: statisticsglobe.com/online-c…
#tidyverse #R #datastructure #RStats
Sergio Civera retweeted
ColabFold 1.6.3 is out! 2.5x faster, pip-installable, ipSAE+pDockQ2 scores. Thanks Choonghwan Lee, Marielle Russo, Gyuri Kim, Martin Steinegger, Milot Mirdita
🐍 pip install colabfold[alphafold]
(1/3)
Sergio Civera retweeted
gget 使ってる?
バイオインフォマティクスでよく使う公共データベースを、Pythonやコマンドラインから簡単に検索・取得・解析するためのオープンソースツール。
gget: Efficient querying of genomic reference databases academic.oup.com/bioinformat…


























