Applications of Computational Biology

Computational biology involves the application of mathematical modeling, computational simulation techniques, data analytics and theoretical methods to the study of behavioral, biological and social systems. When broadly defined, the field includes foundations in applied mathematics, computer science, chemistry, biochemistry, molecular biology, biophysics, genomics, genetics, evolution, ecology, neuroscience, anatomy, and visualization.
Initially, the study of computational biology focussed on the structure and sequence of biological molecules, mainly in an evolutionary context. However, beginning in the 1990s, it extended gradually to the analysis of function. Functional prediction focusses on the structural and sequence similarity between known and known proteins and analyses the interactions of proteins with other molecules. These analyses may be extensive, allowing computational biology to become aligned with systems biology.
Regulatory, biochemical, and genetic pathways are interleaved and branched, as well as dynamic. This calls for sophisticated computational methods for their modeling and analysis. Also, modern technology platforms for rapid generation of biological data have extended the traditional hypothesis-driven testing to data-driven analysis, allowing computational research to be performed on genome-wide databases of unparalleled scale. Many aspects of the study of biology, as a result, have become unthinkable without the power of computers and computer science methodologies.


Production of Life-Long Blood Depends on Many Cells that Form Before Birth

St. Jude Children’s Research Hospital researchers have discovered that production of life-long blood depends on more “ancestor” cells than earlier reported. Published in the journal Nature Cell Biology, the study focused on the origins of blood-forming cells before birth.
Hematopoietic or blood-forming stem cells are responsible for the production of life-long blood. The cells can make any blood cells. Therapeutically, hematopoietic stem cells are used to restore immunity and blood production in patients undergoing bone marrow transplantation for cancer treatment. Understanding how the blood system develops throughout prenatal growth provides insight into the roots of blood diseases that occur early in life.
In the study, St. Jude scientists used a mathematical modeling and color-coded cell labeling system to show blood-forming stem cells in mice arise from roughly 500 precursor cells rather than a few cells. While developments of blood system are the same in humans and mice, the precursor cells in mice are likely at least ten times fewer.
All previous studies had reported that only a few precursor cells take part in determining the blood system. However, the current study has shown that many cells are involved. The findings are expected to help the researchers unravel the origins of disease and find cells that are susceptible to disease-causing mutations.

A Computer Program that Distinguishes Human Cells

Although each of the cells in human body carries the same DNA sequence, there are many varieties of cell types and functions. The differences stem from how the sequence of the DNA is interpreted.
Recent developments in single-cell sequencing are allowing researchers to measure which of 20,000 genes in human is active in each cell. With more than 30 trillion cells in our body, the methods offer an unparalleled level of detail that is transforming research in medicine and biology. But when this technique is applied to numerous cells from various tissues, it turns out to be increasingly problematic to process the huge amounts of data and perceive meaningful patterns.
Stein Aerts, a computational biologist and Professor at the University of Leuven, and his team joined forces with bioengineers, IT specialists, and mathematicians to rise to the challenge. They developed a computer program that detects different types of cells based on their patterns of gene expression. Referred to as SCENIC, the program identifies different cell types quickly and accurately.
The researchers’ technique could help develop a cell “atlas” in the human body. The result is expected to become an invaluable source of information for biology and medicine.

Some 2 Percent of Human DNA is Neanderthal

The genetic legacy of Neanderthal could influence many things from sunburns to cholesterol and bad habits. There was a time when Neanderthals were considered as mindless brutes. However, that idea has long been proven wrong. Neanderthals, in many ways, were just like humans. They were also superior in some ways. Today, anthropologist know that humans and Neanderthals interbred, leaving humans with a percentage of their DNA.
In the new study, computational biologists Janet Kelso and Michael Dannemann looked at the link between DNA of Neanderthal and human behavior and appearance. Their analysis was broad because it included more than 100,000 individuals. However, it was also limited because all the data came from UK Biobank.
The researchers found the Neanderthal genes determine eye and hair color, sleep time preference, and even how badly you sunburn. It may be genes of Neanderthal that control whether you are a night owl or a morning person. However, according to Kay Prüfer, a researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, people should not go accusing Neanderthals of all their woes. She co-authored a different study, in which people living in Western Eurasia were found to carry less Neanderthal gene than people in East Asians.
Prüfer and colleagues conducted a broad, high-quality sequencing of a Neanderthal genome. They studied the bones of a 52,000-year-old Neanderthal woman. They found that genes Neanderthal contribute 1.8 to 2.6% of the total genetic makeup of Eurasian people.