supercomputing

IRP’s Eugene Koonin Elected to National Academy of Medicine

Scientist Decoded DNA to Build a Genomic Tree of Life

Dr. Eugene Koonin

In 1973, the geneticist Theodosius Dobzhansky wrote a now-famous essay that declared, “Nothing in biology makes sense except in the light of evolution.” That sentiment has served as the guiding principle for the career of IRP senior investigator Eugene V. Koonin, Ph.D., who was elected to the National Academy of Medicine (NAM) in October 2022 for his contributions to the field of evolutionary biology.

Dr. Koonin’s pioneering efforts to identify clusters of similar genes found in different organisms passed down by a common ancestor — known as ‘homologous’ genes — has helped to unlock the secrets encoded in DNA and create a foundation for the systematic study of how genes evolve and function. His lab at the National Library of Medicine’s National Center for Biotechnology Information (NCBI) uses a combination of genomic sequencing and mathematical modeling to compare genes across species and determine how they work and where they came from. From this information, his team can develop a systematic framework to show the relationship between genes as they evolved. It’s like drawing the tree of life, but on a genomic scale.

A Computational Approach to Curbing Chemotherapy’s Side Effects

Study Identifies Compounds That Could Aid Body’s Removal of Toxic Cancer Drugs

computer binary code

When it comes to cancer, the treatment can sometimes feel worse than the disease. Not only do chemotherapy drugs cause grueling side effects, but certain products made by otherwise benign bacteria living in our digestive system can interfere with the body’s ability to get rid of those toxic chemicals. A new IRP study used a cutting-edge computational approach to help identify compounds that inhibit one of those meddling bacterial molecules, which could eventually lead to the creation of medications that reduce some of chemotherapy’s side effects.

The Virus vs the Machine

IRP Leverages Supercomputing to Combat Coronavirus

rows of computer servers

Over the past six months, a tiny virus has completely upended life in the United States and many other countries. To combat this microscopic threat, some IRP researchers have turned to a tool the size of a small building.

Biowulf, the NIH’s supercomputer, is supporting more than a dozen different IRP research projects focused on the novel coronavirus. As the world’s most powerful supercomputer solely dedicated to biomedical research, Biowulf allows scientists to analyze data and run simulations at unprecedented speed. Two weeks ago, a blog post described how IRP investigators are using Biowulf to elucidate the structure of the novel coronavirus and simulate how potential therapeutics might interact with it. Picking up where that post left off, this blog will explore the application of Biowulf to important questions about the spread of COVID-19 and the way that its genes, along with our own, might influence its impact on the body.

IRP Supercomputer Enables Rapid Response to Coronavirus

Biowulf Lends Massive Computing Power to NIH Research Efforts

rows of computer servers

Nations around the world are bringing every weapon in their arsenals to the fight against the COVID-19 pandemic: vaccines, new and existing therapeutics, personal protective equipment like face masks, and enough hand sanitizer to fill the Atlantic Ocean. The NIH community is contributing to this unprecedented effort with a tool that no other research institution can claim: Biowulf, the world’s most powerful supercomputer solely dedicated to biomedical research.

Plugging the Gaps in the Human Genome

Supercomputing Helps IRP Researchers Complete Our Genetic Blueprints

DNA sequence

While the Human Genome Project accomplished a remarkable feat in sequencing all the genes in the human genome, technological limitations still left significant swaths of our genetic blueprints unexplored. Recent advances in DNA sequencing are starting to fill in those gaps, but these new technologies require new computational tools to make sense of the data they generate. That’s where computer scientists like the IRP’s Adam Phillippy, Ph.D., come in.

Supercomputing Pushes Pregnancy Research Forward

mother with baby

Virtually all parents would agree that having kids is a massive undertaking, and not just after they’re born. Many couples struggle to conceive, and each year thousands of American women experience complications when giving birth. With the help of the NIH’s state-of-the-art supercomputer, Biowulf, IRP senior investigator Rajeshwari Sundaram, Ph.D., develops and refines statistical tools that can guide prospective parents and their doctors through these challenges.