Webinar about the GAN I developed for my Master’s thesis

I have recently had the pleasure to talk about the project that I developed for my master thesis in the group of Fernando Racimo, at the University of Copenhagen. I was invited as a speaker in the Bioinfo Club April 2022, wonderfully organized by BioinformaticsGRX (https://bioinformaticsgrx.es/).

BioinformaticsGRX is an association of young bioinformaticians promoting and disseminating their love for all things bioinformatics in thousands of different ways: webinars, round tables, symposiums, workshops, etc…

And their headquarters is in Granada, my hometown!

You can find the recorded video of the webinar below:

https://www.youtube.com/watch?v=dko-bEcEb20&t

(warning: it gets tech-geeky!)

My poster at the Single Cell Symposium

The Single Cell Symposium was a blast! It was great to attend this conference in person, now that it seems the covid is giving us some room to breathe (literally).

I could finally get to physically meet renowned scientist that I have been following in social networks for long time, and the surroundings of the Barcelona Biomedical Research Park building where the meeting took place were idyllic. Just to show you a peek of the views from this institute:

prbb

The talks were held from top national and international researchers in the single cell universe, and they were all very inspiring. During the poster session, I presented my poster on DeepSCore, a deep learning framework that I am developing to easily annotate multimodal single cell datasets in both Python and R using a curated reference.

It got much more attention than I expected! I literally was discussing my results to visitors the whole time. Lots of them were interested in applying my tool in their analyses, and I even got proposed to add DeepSCore in a Python single cell tool ecosystem in the future. Discussions got funnier when beers were served at the bar.

poster

While being a bioinformatics scientist can feel like a lonely trip sometimes, where it’s basically you and your computer fighting with each other, these kind of days are the ones where you can see the outreach and effects of your efforts in the outside world. And it feels really satisfying.

If you’re interested in reading my poster with higher detail, you can find the PDF version here:

deepscore_poster.pdf

Come say hi at the Single Cell Symposium!

Hi frengers! (not quite friends, but not quite strangers)

I will be presenting a poster at the coming Single Cell Genomics Symposium in Barcelona on March 24th and 25th! I will take place at the PRBB, Parc de Recerca Biomèdica de Barcelona. If you are reading this and are attending the event, come and say hi!

In my poster I will show my latest advances in developing DeepSCore, a multi-language (works in R and Python) and multi-omics (works with gene expression and genomic regions) deep learning model to automatically annotate single-cell datasets.

I will update this post with more information about it soon.

Stay tuned!

Current research: ESPACE project

The Human Cell Atlas (HCA) has the mission to create a comprehensive map of all human cells, as a basis for both understanding human health and diagnosing, monitoring, and treating disease. Inside this initiative, the ESPACE (“Expression and Spatial analysis Pancreas Atlas Consortium Europe”) consortium is born.

Right now, I am busy collaborating with different groups of Barcelona and Berlin in a “Hackathon”. Our main goal is to integrate and harmonize different data modalities at single-cell resolution to pave the way towards a holistic atlas of the human pancreas in health and disease.

More specifically, I am in charge of the scATAC data modality, which describes the chromatin accessibility landscape of each sequenced cell. This will give us an insight on the regulatory mechanisms that drives the characterization of the different cell-types in the pancreas, like which promoters are differentially accessible in different cell states or which distant trans-regulatory element could be influencing a certain gene expression.

espace_schematic

We are planning to have an interactive visualization tool where anyone can freely explore the data we are curating.

Hope to show you more on this very soon!

Meanwhile, you can find all the information related to ESPACE here:

espace-h2020.eu

Present and future of my blog

Welcome to my site! I have created this site with the purpose of collecting several of my passions in one same place, in the way that can act as a personal portfolio.

Here, I plan to update the state of my computational research, as well as some bioinformatics topics (or scientific topics in general) that I find interesting.

Apart of that, I also would like to share non-sciency stuff. This can be an absurd philosophical realization that came across to my mind while going for a walk, my critical view on the latest Oscar-winning movie, or my latest amateur musical composition that I share in the section music.