Computational Systems Biology Lab

by Nature India

The algorithm — minMicrobiome — could help design personalised treatment strategies for gut microbiome-related diseases, for example by reintroducing lost gut flora in some cases of severe inflammatory bowel disease and Clostridium difficile infections. It could also optimize industrial processes such as chemical production and wastewater treatment, say scientists at the Robert Bosch Centre for Data Science and Artificial Intelligence at Indian Institute of Technology Madras in Chennai.

by Aditi Jain

Although, there does exist tools that identify personalized cancer genes, however, they use unsupervised learning method and predicts based on the presence and absence of mutations in cancer-related genes. This study, however, is the first one to use the supervised learning method by applying gene-based labelling that is cancer-specific. This new model also takes into account the functional impact of the mutations while making predictions.

“ The research area of precision medicine is still at a nascent stage. PIVOT helps push these boundaries and presents prospects for experimental research based on the genes identified,” says Malvika Sudhakar, lead author of the study.

by Akshay Anantharaman

In this study, the authors of this paper —Mr. Priyan Bhattacharya and Prof. Arun K. Tangirala from the Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai, India, and Dr. Karthik Raman from the Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India—have for the first time suggested a generic systems-theoretic approach to unravel the possible networks design configurations for perfect adaptation.  The proposed approach translates the conditions for biological adaptation into precise mathematical equations using systems theory. Further, these equations are mapped back to necessary structural requirements with the help of combinatorial mathematics.

by Akshay Anantharaman

A lot of research is happening with regard to cancer, and thankfully, a lot of progress has been made in understanding the aetiology of this complex disease. “Driver” genes are known to play a major role in causing cancer. Many of these genes have been identified, but still many driver genes need to be identified. Till now, only genes that harbour a high rate of mutations, thus causing cancer, have been identified. But what about the numerous driver genes that haven’t been identified?

by Aditi Jain

“A classic challenge in biology is to study the function of proteins. Of various functions, essential functions are very interesting, as they map to important indispensable genes in an organism. Experimentally identifying these genes is rather expensive and challenging. Computational predictions can help point in the right direction, to prioritise experiments. To date, experimental data are available for <100 organisms! On the other hand, sequencing data are available for 1000s of organisms, as also interactome (networks of interactions) data. In the paper, we posit that network information is crucial to predict essentiality and achieve excellent performance in prediction, by simply using network data,” explains Dr. Raman.

by Aditi Jain

Dr. Karthik Raman’s research team from IIT Madras has been working to understand the role played by a specific class of bacteria called Bifidobacteria in the human gut. Recently, they published their research findings in the journal Scientific Reports. Members of Bifidobacteria had earlier shown to be present in the intestine and oral cavity of humans, intestines of insects and in sewage. These bacteria have a number of enzyme-coding genes associated with the metabolism of complex and non-digestible carbohydrates such as milk and plant fibers. They are also known to produce vitamins and antimicrobial substances, regulate the immune system, perform anti-obesity and anti-inflammatory activities which piqued the team’s interest in bacteria.

by Gayathri Sambamoorthy (and Karthik Raman)

One student questioned me, “Is your research about the evolution of microorganisms?” I smiled in happiness that she got something from what I spoke! “Great! Not really! I am coming to that! My research is about understanding how evolution alters reactions in an organism. When the microorganisms evolve, new reactions are added to the pathways. When I mean evolution, it doesn’t just have to be the addition of new reactions. There can also be the removal of reactions from the pathway if the organism thinks it is of no use anymore!”

by Gayathri Sambamoorthy (and Karthik Raman)

Yamini, a class V student, is a very playful child who keenly observes everything around her and comes up with multiple questions that intrigued her. One morning she was angry with her mother that she did not permit her to play in the sand. Seeing the energetic kid unhappy, the teacher took the time to ask her about it.

After Yamini narrated, the teacher decided to explain, " Your mother is right! You may fall sick because of the microbes or microorganisms present." Yamini, confused and curious, said, “I don’t see anything in the sand. How will I fall sick?” The teacher explained, “Microorganisms are small creatures that exist everywhere, and we cannot see them. We can see them only through a microscope!”. She explains and adds further, “There are both harmful and harmless microorganisms.” “What do they eat? They are so tiny!” exclaimed Yamini!

by Aarthi Ravikrishnan

Ever wondered how food gets digested? How does milk curdle? How do plant litters decompose? Such questions have intrigued me, and I have always wondered what went on behind the screens. Who played a role? Who performed these actions? Was it someone as giant as the Hulk or as tiny as a Lilliputian? Being a biologist, I decided to view them through a magnifying glass (“microscope”) and discovered these complex actions were carried out by tiny little creatures called “micro-organisms”. These micro-organisms are akin to human beings; sometimes they choose to remain single and isolated, while many-a-time tend to stay together as a part of a community. And during their times together, they exhibit the same characteristics as any human being would do: Compete, Cooperate or both.