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Hi! I’m Daria, ChromRare PhD student enrolled in the project on the side of an industrial partner – geneXplain GmbH, German bioinformatics company. After spending over 10 years in the industry, I find it extremely exciting to have this opportunity of being enrolled in an academic study of my PhD program on the premises of University of Trento. This unique ability to dive from the industrial R&D to the academic environment during my secondments within the ChromRare project has opened to me a broader understanding of the complex interplay between different areas of computational and wet lab biology. 

I did and still do experience quite some challenges in learning biological insights (as a mathematician by training), but I truly enjoy this journey that definitely shifts my knowledge and understanding of disease molecular mechanisms to a new level.

At the project my role is in development software pipeline for multi-omics analysis of the data produced by the project partners. The end goal of my study is in modeling of the cell differentiation process in chromatinopathies in order to understand how pathogenic variants in chromatin regulators may lead to impairments of cell differentiation process. 

Since project data is still in the process of generation, at the moment I am testing my software pipeline on the open access datasets on Charge and Kabuki syndromes. Already now, based on the analysis of DNA methylation data in Charge and Kabuki syndromes, I was able to detect key mechanism similarities and differences of these two chromatinopathies. Having modeled molecular mechanisms of these complex rare genetic diseases, I have pick pointed potential master regulators of these pathologies on the level of intracellular reactions. I am now looking forward to working with the data generated within the project, meanwhile proceeding with further development of my software system (by the way, you can check it out at geneXplain’s website – the pipeline is called Genome Enhancer and it is truly an awesome solution for those who need to integrate various omics data in one study).

#PhDLife #Epigenetics #ComputationalBiology

Working on my PhD project is often like studying a vast and intricate picture. Each data set – RNA-seq, ChIP-seq, Micro-C – reveals a fragment, a brushstroke full of significance, but also incomplete on its own. The real challenge is taking a step back to see how these individual lines connect, forming a bigger picture of neural crest development and its disorder in Cornelia de Lange syndrome.

Data integration is more than a technical task: it is an act of interpretation that requires a constant shift between detail and perspective, between the molecular signature of a single enhancer and the orchestration of entire regulatory networks.

I am Lucio Di Filippo, a PhD student committed to understanding how changes in chromatin architecture and epigenetic regulation converge to shape developmental outcomes and how their misregulation leads to disease.

#PhDLife #Chromatin #Epigenetics

Different fields of science are like different languages. The deeper you go into a specific field, the more it feels like speaking a unique dialect. Scientists from different disciplines can generally understand one another and pick up a word or two, but it’s still a different language. Anyone who has learned a new language knows the incredible feeling of finally being able to express themselves comfortably—engaging in passionate discussions, cracking jokes, and truly connecting.

That’s exactly how I felt as part of the Chrom_Rare consortium. It was like finding people who speak the same dialect as me, and what a joy this past year has been! I’ve had the opportunity to travel to new places, meet incredible people, and work on cutting-edge science.

Of course, this journey hasn’t always been smooth. There were days when nothing seemed to work, making me feel like an imposter. But thankfully, those moments have been few and far between. Often, it feels like a never-ending video game: as soon as I master one skill to push my project forward, five new challenges appear, each demanding to be conquered. But I take it one step at a time, eager for what’s ahead.

I am Yunna Erika Strøm, a doctoral candidate in the MSCA Project Chrom_Rare. My passion lies in unraveling the wonders of chromatin dynamics through mass spectrometry-based proteomics, with a special focus on a technique called Proximity Labeling.

#PhDLife #LabDiaries #ChromatinBiology #Epigenetics #ResearchRollerCoaster #GrowthThroughScience #MSCA #EUHorizon #ChromRare

Hi, I’m Emile, and I joined ChromRare to study the epigenetic mechanisms that govern developmental programs, aiming to better understand Kabuki Syndrome. This first year of PhD has been a mix of challenges, adventures, and a lot of exciting learning.

First, going from the calm of Strasbourg to the great entropy of Naples was a real change. But despite the initial impression of chaos, I felt incredibly welcomed and quickly found myself at home. A year later, I can honestly say that I’ve never loved a city so much, and I’m glad I was able to learn Italian.

Then, my first steps in the lab weren’t always as smooth as I expected, for example I learned that it can take some time and effort to obtain the cell lines of your dreams. And when it came to analysing the first data… I have to say that my bioinformatics skills were almost non-existent. I could barely open a spreadsheet in R, and analysing OMIC data seemed out of my reach. But thanks to courses, the help of colleagues, and a lot of trial and error, I managed to carry out my first RNA-seq and ATAC-seq analyses from scratch.

Looking back, I realize that I learned a lot!

After the ups and downs of the start, I feel on the right track and I’m very excited about the next steps.

#PhDLife #LabDiaries #ChromatinBiology #Epigenetics #ResearchRollerCoaster #GrowthThroughScience #MSCA #EUHorizon #ChromRare

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Working in a research lab as a PhD Scholar feels like riding a rollercoaster—a thrilling mix of highs and lows. There are days when that perfect fluorescence signal brightens not just your image but your smile and you are finally acquiring the data you have been chasing for weeks.
And then, there are the lows—the days when experiments refuse to work, when cells behave strangely, and the frustration of troubleshooting and repeating the experiments is (photo)bleaching your enthusiasm. Yet, amidst this chaos, I can feel the journey transforming me— learning how it is not just about experiments and generating data; it’s about how to navigate challenges, uncertainty and setbacks, and how to embrace failure as an essential part of growth.

Steering this roller coaster (partly), I am Shiza Nasir, doctoral candidate in MSCA Project Chrom_rare;
studying mechanisms underlying chromatinopathies, particularly how nuclear mechanics and chromatin organization contribute to pathogenesis.

PhDLife #LabDiaries #ChromatinBiology #Mechanobiology #ResearchRollerCoaster #GrowthThroughScience #MSCA #EUHorizon #ChromRare