Bioinformatics

How AI is Making CRISPR Gene Editing Safer

Contributors: Kaviya V, Nithya M, Subhathi B

Am I Hallucinating or Can AI Now Design Cancer-Curing Antibodies?

AlphaFold2 Hallucinated to make a new Cancer Antibody

How to Perform Large-scale Data Processing in Bioinformatics

A Complementary Discussion for “Ten Simple Rules for Large-scale Data Processing”

Molecular Dynamics is Amazing — So Why Isn’t Everyone Using It?

For decades, molecular dynamics (MD) simulations have served as one of the most powerful microscopes in modern science — allowing us to…

What is Computational Biology?

Using computers to solve puzzles in nature? This is still a bit tricky for some to grasp.

If I were focusing on protein modeling back then…

I might be stumbled into different world of AI nowadays.

Nobody is Reading Your Supplementary Files

Why computational biologists need to start building products!! Part-4

From Proteins to Pipelines: How Open-Source Nextflow Tools Are Accelerating Drug Discovery

Written by Jelena Pejovic, Senior Bioinformatic Engineer and Jorge Moura Sampaio, Bioengineering Lead

Cloud-native Hello World for Bioinformatics

So often the first task my customers ask me to work with them on is to ‘cloud-scale’ their computational complex tool or data pipeline. I…

When the Finish Line Keeps Moving: Why Bioinformatics Feels Like a Race You Can’t Win

In a field where methods evolve faster than memory, reproducibility and collaboration aren’t just nice to have; they’re how you survive.

Reproducing Research Papers and Surviving ChIP-Seq

You’ll figure out which types of graphs are best for different datasets (because not all data should be squeezed into a bar graph). 📊

A Simple Introduction to Functional Genomics

Knowing the genome sequence is one thing. We’re also interested in what each chunk does, how, and why. Functional genomics is the answer.

Gene Expression and Network Analysis of COVID-19–Associated Thrombosis Using the DICE Algorithm

As I briefly introduced the DICE algorithm in my previous article and its differences from traditional differential expression analysis…

Building a “Truth” Dataset for Bioinformatics Method Development

What do you do when the research problem you aim to explore with deep learning lacks a gold-standard dataset? You create your own; like me.

Rethinking Bioinformatics

Solving the Challenges of Traditional Pipelines

Fine-Tuning ESM-2 for Protein Subcellular Localization: LoRA Matches Full Fine-Tuning with 2.4%

New Paper Highlights Results from Recent PrecisionFDA Truth Challenge

Scientists from DNAnexus, the Genome In a Bottle consortium, and other institutions have published a paper in Cell Genomics that shares…

Beyond PAM and BLOSUM: How Protein Language Models Are Changing Mutation Prediction

We all encounter BLAST, PAM, and BLOSUM during our studies in biotechnology or bioinformatics. The process is straightforward: take a…

About Me

Hi, I’m Ozlem, a bioinformatician in Bonn, Germany, working at the intersection of biology and data science. My work focuses on applying…

ProteinGym: A Unified Benchmark for Protein Fitness Prediction

The Problem with Benchmarking in Computational Biology