frontier in bioinformatics
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These days, corporate entities are increasingly dominating research in basic science. This essay looks into how this will change the most cherised convention of science. Researchers follow many conventions. In the short term, graduate students learn these conventions from their seniors and follow them without question. Over time, those students grow up as senior researchers and modify the…
I came across an interesting blog post titled Biology is Messy . The main argument is that biology is not built on top of reductionist theories, and the current push to collect large amount of data and use “AI” to “solve” biology is not likely to lead to finding reductionist theories either. Instead we will get a bunch of overfitted models hyped up as “solutions” by corporate entities. I agree…
Right now everyone is either enamored of or is completely turned off by AI. Speaking of being fed up, please check the students at University of Florida booing at this commencement event . Much of their reactions comes from intense hype generated by the tech-bros of Silly Con valley to increase stock prices of their companies. Instead of emotionally swayed by hyped-up projections, let us learn the…
On the subject of reconstructing gene regulatory networks (GRNs) from RNAseq and scRNAseq data, I am working through a number of review papers and the techniques described therein. Gene Regulatory Network Inference in the Era of Single-cell Multi-omics - review paper published in 2023. Gene Regulatory Network Reconstruction: Harnessing the Power of Single-cell Multi-omic Data - published in 2023.…
In an earlier post , I divided the modern era of genetics into 18-year periods (eras). The discoveries of each era opened new questions and provided fuel for the next era. In the most recent era (2003-2020), biologists moved from working on individual genes to whole genome experiments, performing single-cell experiments instead of measuring gene expressions in many cells in aggregate and also…
In my earlier post , I mentioned about three distinct activities described under the broad term “AI”. They are - (i) using web-based text engines like Chatgpt, Claude or Gemini and their extensions as coding tools, (ii) downloading numerical models directly from Huggingface and building applications on top of them, and (iii) developing and training mathematical models for new applications. Maybe…
I have decided to divide the last 70-80 years of genetics into different eras. Each period started with a set of burning questions, which were resolved by the end of the era. However, those answers created another set of burning questions to be resolved by the newcomers to the field. Please tell me whether you agree my classifications, and what you expect the current era to be like. 1949-1966 -…
In 2011, I wrote two articles ( here and here ) providing beginners’ guides to bioinformatics. Eight years later (2019), I posted an updated guide here . Now that AI has become a powerful tool, it is time to discuss how the work of bioinformatics and computational biology is changing. Before continuing, I will mention that three distinct activities fall under the broad term “AI”. They are - (i)…
I have been coding with AI assistance for about six months now and more actively since late December 2025. If I had to compress the entire experience into a single sentence, it would be this: AI made me faster first and then it made me slower. Let me explain. How I Started Like most people, I began small. I needed a specific customization in a plot generated by ggplot. Instead of going through…
In the earlier posts of this series ( here , here , here and here ), we covered the mathematical and biological aspects of evo and evo2. One important topic that we have not covered yet is how the models were trained. What is training? The AI or deep learning models, or as we prefer to call “Massively Parameterized Statistical (MPS) Models” , are mathematical functions with a large number of…