"[commit 1 percent of profits for workers re-training] isn’t charity. (...) Helping retrain workers is common sense, and such a small ask that these companies would barely feel it, while the public benefits could be enormous." www.nytimes.com/2025/12/27/o...

Today, I inaugurate a new Github repository: github.com/andrebolerba... I created this to store code that, although short and simple, may be useful for addressing specific needs and challenges.

I am very proud to announce that yesterday I have successfully defended my PhD. It was a long journey, filled with difficulties but with a dose of rewards - scientific, professional but most of all, personal. But, it definitely made me a better scientist, and a better person.

"(...) the rise of generative AI in bioinformatics has not diminished my role, but redefined it. It has challenged me to become a better scientist. For good or ill, AI seems to be here to stay. I urge you to embrace the technology — not to replace your expertise, but to amplify it. #bioinfo

Can't advise this lab more. If you'd like to work in a curious-driven and nurturing environment, with a high focus on robust data analysis, don't even think twice! #bioinfo #datascience

Last week, I was fortunate enough to watch a talk from @tkorem.bsky.social , where he presented different things, from addressing inter- study variability on microbiome projects to the use of novel approaches on metagenomics alignment and processing. Interesting and very relevant! #bioinfo

"GlucoStats demonstrates high efficiency in processing large-scale medical datasets in minimal time. Its modular design enables easy customization and extension, making it adaptable to diverse research and clinical needs" bmcbioinformatics.biomedcentral.com/articles/10.... #datascience #biostats

"Delphi-2M predicts the rates of more than 1,000 diseases (...), with accuracy comparable to that of existing single-disease models. Delphi-2M (...) also enables sampling of synthetic future health trajectories" www.nature.com/articles/s41...

Amazing repository with several references and resources for scRNASeq analysis github.com/crazyhottomm... #bioinfo #singlecell

"Even if work is done by or with the help of experts (...), it is crucial that researchers understand how a method works, that they can assess data quality, and that they fundamentally understand what types of conclusions can and cannot be drawn from their data" www.nature.com/articles/s41...

Spreadsheets represent an everyday tool for most wet-lab scientists. So, why not use them at their highest potential, efficiently and ready for open science? This paper provides some recommendations for the use of spreadsheets: www.nature.com/articles/d41... #bioinfo #stats

FlyBase, a Drosophila database, will lose a third of its team in early October because the Harvard grant that covered the employees’ salaries was canceled. Scientists warn that losing FlyBase could devastate fly research. By @claudia-lopez.bsky.social www.thetransmitter.org/community/ha...

1/n Because, in bioinformatics, sharing is caring, let me share something I have recently started exploring - graph mapping and pangenome graphs. A pangenome graph encodes a reference genome built from many genomes in one structure, thus trying to encapsulate the known genetic variability.

1/n Brief guide to statistical analysis of grouped data in preclinical research www.nature.com/articles/s42... In preclinical studies, clustering and nesting (C&N) scenarios, such as group-housed animals or cells on a single plate, are frequently found. This has important statistical implications

Instead of painstakingly dissecting a set of primary data to find novel patterns, it can be more effective to fit an unsupervised cluster-factor-latent-spaces model and then painstakingly dissect the model parameters to find patterns imposed by the model inference.

Very interesting paper from Soares lab @gimmfoundation.bsky.social

Reposting this a single time feels too short to show how much I agree with this

gimm.pt/jobs/researc... Great job opportunity for any bioinformatician out there! @gimmfoundation.bsky.social #bioinfo

Some thoughts about rarefaction adaorg.github.io/datamisfits/...

'One possible strategy is to organize consortium-led initiatives that integrate and curate reference datasets, establish criteria for dataset transparency, and mandate standardized preprocessing pipelines to reduce the variability in how competing models are evaluated' www.nature.com/articles/s41...

Quando se corta na ciência When science is cut Instamos os políticos a reconhecerem que a ciência não é um interruptor que pode ser ligado e desligado sem consequências profundas e duradouras. www.publico.pt/2025/... 1/2

Taking the opportunity to repost this since people hate it BECAUSE I'M RIGHT.

GIMM is on Bluesky! We're a recent research foundation created by the merger of 2 leading research institutes in Portugal, IGC and iMM, dedicated to answering fundamental questions of biology and human health & developing solutions to improve health and promote local and global equity. Visit gimm.pt

Bluesky is indeed a social network on the rise. Another project with amazing potential is the new Portuguese institute - Gulbenkian Institute of Molecular Medicine (GIMM) - gimm.pt. I have created a Starter's pack for the GIMM Team, to link with each other and with the world go.bsky.app/RACwsRN

Glad to see my institute @gimmfoundation.bsky.social on bluesky! Check up the account, and definitely follow them! Good things will be popping up frequently

Hi folks! I'm looking for a good and easy to use pipeline to annotate genomes from RNA-seq & protein data. Any suggestions? (I've already tried BRAKER3, I was wondering if people were using other tools out there...) 🧪

Bluesky is indeed a social network on the rise. Another project with amazing potential is the new Portuguese institute - Gulbenkian Institute of Molecular Medicine (GIMM) - gimm.pt. I have created a Starter's pack for the GIMM Team, to link with each other and with the world go.bsky.app/RACwsRN

Working on a case study for survival analysis. These models are odd compared to typical GLM examples: missing data (censoring) that cannot be ignored, data model (likelihood) and data-generating model not same, how to visualize predictions, 2+ equivalent ways to program. Good real data wrestling.

In the advanced data analysis unit @GIMM, we have discussed sharing our experiences in checking, filtering and analysing data (omic and otherwise). So we decided to create a blog! adaorg.github.io/datamisfits/

1/🧵Calling all container users! Whether you're a bioinformatician, developer, or a curious enthusiast, if you’re working with containers you need to check this out 🚀 Let me introduce you to Seqera Containers—a game-changer for building & hosting containers for free. 👇 https://buff.ly/3Oo8UG9

💻Webinar: A new era for @nextflow.io! Join us on Dec 10 to explore the latest major version of the Nextflow VS Code extension, now powered by a new language server that elevates Nextflow into a first-class language in its own right! 👉 Register now: hubs.la/Q02Z0R0q0

p-value and null hypothesis testing: Where does it come from, where are we and where should we go from here: 1/n Despite being used throughout the 1700's, the p-value concept shows up in the 1900's by Karl Pearson and his Pearson's chi-square. But, the big boost came from Fisher

A gentle introduction to pangenomics https://academic.oup.com/bib/article/25/6/bbae588/7902219

Forest plots as an interesting tool to reporting results instead of just p-values. towardsdatascience.com/unhappy-with... #stats

I made one for stats papers

1/n Good alternatives for the p-values as major deciders of hypothesis validity are needed, either from a conceptual or from a methodological point of view. For the latter, I have been a great fan of this paper: www.nature.com/articles/s41...

"The ultimate goal of these approaches is to capture the complex interactions, dynamics and influences of microorganisms that can shed light into the mechanisms underpinning health and disease." academic.oup.com/bib/article/...

R lesson of the day (as most lessons, found completely by chance). When using ordered function in R instead of factor to created ordered factors, it will **definitely** have an impact in subsequent modelling you perform! 1/n

www.nature.com/articles/s41... "A rinse-and-repeat iterative approach whereby experimentalists and modelers work closely together and learn each other’s language12 should help continue to shift focus from seeking correlations to exploring causation."

Why you should "rehearse" your analysis before collecting the data towardsdatascience.com/why-hypothes... #Stats

As a part of the Advanced Data Analysis Unit of the GIMM institute, I have worked with some transcriptomic datasets. Considering I have faced different data types, scenarios and analysis requirements, I have decided to create a github repository for RNASeq analysis. github.com/andrebolerba...

Have you ever faced a problem when working with dates in R, specifically when Excel decides your date is a number? Worry no more! We at the Advanced Data Analysis Unit in the GIMM Institute have developed a function to work around this problem: github.com/andrebolerba...

(Re)Introducing myself: I'm a data enthusiast within the realm of biology, play around with #bioinformatics in addition to #rstats! Currently working my way into #python!!

A simple, yet super relevant explanation on some interesting statistical concepts towardsdatascience.com/a-visual-exp...

"Failure to consider sex and gender in research and clinical care contributes to health inequities and, in particular, poor understanding of women’s health" www.nature.com/articles/s41...

On the importance of statistics - 1/n From a practical perspective, statistics encompasses experimental design, visualization, inference and prediction. Under a more philosophical lense, though, it presents the world as we perceive it, and quantifies uncertainty of said view.

For anyone performing statistical analysis, in ecology or in any other field, this is incredibly relevant! besjournals.onlinelibrary.wiley.com/doi/10.1111/...