Back to Writing: Some Thoughts on Machine Learning
Hello. Finally, I’m back to writing on the blog. Intense work commitments and plenty of unexpected events have limited the time I could spend studying and sharing with you my progress in the world of bioinformatics and, more generally, in data analysis. But today, despite the huge backlog of work I still have, I really…
Linear Regression Made Simple (and Sketchy!)
Hi everyone! How are you doing? Today the sun is shining, and after some gym time and work, I finally found a moment to write a long article I’ve been wanting to share on my blog. You know, Andrew Ng has often stressed the importance of deeply understanding the fundamentals of machine learning to become…
Dive into pre-transcriptional regulation analysis
Hello. How are you? I’m a little sad. These days I had an idea of applying ML models in bioinformatic field. The idea is good but moving from idea to practical application is always complex and often models do not learn as we hope. In short, I am a little in down, but this is…
Beyond Data Analysis: The Bioinformatician’s Role in Planning RNAseq Experiments
Hi, how are you? We’re approaching spring and brighter days, and that generally puts me in a good mood. At work, I’m enjoying learning new things and improving as a bioinformatician; the more days of work I put behind me, the more experience I accumulate, and with it, my imposter syndrome decreases. In this recent…
Exploring Principal Component Analysis (PCA)
<script type="text/javascript" async src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/MathJax.js?config=TeX-AMS_HTML"> Hello! I finally found some free time to get back to writing on my blog. Have I ever told you how I ended up becoming a bioinformatician (or rather, how I started hoping to become one)? I graduated in Agricultural Sciences and later earned a Master’s degree in Plant Biotechnology. I…
Comprehensive Guide to ATAC-seq Data Analysis
A small disclaimer !!!!! At the bottom of the page, you’ll find an important message for the community. So I encourage you to enjoy the article and then, once you’re done, take a moment to read the message I’ve written for all of you. Bye, and happy reading! Overview: 1) Introduction to ATACseq 2) Quality…
Unveiling Hidden Patterns in Data: An Introduction to Topological Data Analysis
Introduction: A Challenge in Clinical Data Analysis Imagine being a researcher in a hospital tasked with analyzing the data produced within its walls. In no time, you would find yourself overwhelmed with clinical data, medical images, population statistics, multi omic gene expression data, and much more. Feeling overwhelmed is natural, especially when you are expected…
Comprehensive Guide to ATAC-seq Data Quality Control
There are several methods to study chromatin accessibility, aiming to understand gene expression regulation at the pre-transcriptional level. One such method is ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing). This technique investigates genome-wide accessibility by leveraging DNA fragmentation mediated by the Tn5 transposase dimer, which binds to chromatin regions typically free of nucleosomes. Recently, I…
How to interpret the TF footprint plot?
Analyzing scATAC-seq data with the Signac toolkit is fascinating because it allows us to obtain several interesting results. Among these, I find the results from TF footprint analysis extremely useful because they allow us to probabilistically estimate the activity of various transcription factors without having to perform multiple ChIP-seq experiments. In this context, ChIP-seq could…
Sequencing in Bioinformatics
I love my job as a bioinformatician, don’t get me wrong, but it can be really frustrating. It’s a job that truly tests your patience, where stress is a daily occurrence. In this field, you quickly realize how much you still need to learn, and that can be discouraging—there’s never a point where you’ve “arrived.”…
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