Research

blogs

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Finding the microbial heroes
by Karthik Raman, Aswathy K. Raghu & Indumathi Palanikumar The algorithm helps in identifying the smallest groups of microbes, capable of executing a desired function, from a large microbial community Given a large co-operative microbial community, an algorithm to identify the smallest subsets of that community capable of a desired functionality is presented. These subsets, called minimal microbiomes, will contain the keystone species that achieve the required purpose. Read the full blog article at https://communities.
• Jul 10, 2024
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Research Highlight: Hunting for mini gut microbe clusters
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.
• Jul 5, 2024
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Towards Personalised Cancer Treatment
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.
• Jul 21, 2022
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A Strategy To Make Networks More Resilient To Attacks
by Aditi Jain “A variety of technological networks form the backbone of modern world infrastructure, and it is very essential to build safeguards to protect these networks against both failures and targeted attacks,” says Dr Karthik Raman, Associate Professor at the Bhupat & Jyoti Mehta School of Biosciences and a core member of the Robert Bosch Centre for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras. Dr Karthik Raman and his student Mr.
• Jun 16, 2022
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Discovering Cellular Networks for Biological Adaptation
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.
• May 11, 2022
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The Hidden Drivers: A Lens into Cancer
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.
• Mar 22, 2022
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CAMP: The Perfect Bacterial Matchmaker
by Aditi Jain Dr Karthik Raman, an Associate Professor at IIT Madras and a core member of RBCDSAI, is a scientist whose interest lies in discerning the dynamics of microbial interactions to utilize them for biotechnological application. Recently, Dr Raman and a post-doctoral fellow in his group, Dr Maziya Ibrahim proposed a computational approach named CAMP(Co-culture/Community Analyses for Metabolite Production) which suggests how to bundle two or more bacteria together, forming a community that produces the desired products in maximum quantity.
• Mar 8, 2022
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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.
• Jan 13, 2021
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Do you desire good digestion? These small bugs in your gut may help!
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.
• Feb 21, 2020
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The road not taken: Part II
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.
• Jan 1, 2020
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The road not taken: Part I
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!
• Jan 1, 2020
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Into the microbial world: Navigating through metabolic maps
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”.
• Sep 6, 2019
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publications

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Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Jonathan L. Golob*, Tomiko T. Oskotsky*, ..., The Preterm Birth DREAM Community, ..., James C. Costello, Marina Sirota*,

Cell Reports Medicine

5:101350
10.1016/j.xcrm.2023.101350
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Bayesian Optimal Experiment Design for Sloppy Systems

Prem Jagadeesan, Karthik Raman*, Arun K. Tangirala*,

IFAC-PapersOnLine

55:
10.1016/j.ifacol.2023.01.026
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Cell-to-cell and type-to-type heterogeneity of signaling networks: insights from the crowd

Attila Gabor†, Marco Tognetti†, Alice Driessen, Jovan Tanevski, Baosen Guo, Wencai Cao, He Shen, Thomas Yu, Verena Chung, Single Cell Signaling in Breast Cancer DREAM Consortium members, Bernd Bodenmiller*, Julio Saez-Rodriguez*,

Molecular Systems Biology

17:e10402
10.15252/msb.202110402
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Mycobacterium tuberculosis (Mtb) lipid–mediated lysosomal rewiring in infected macrophages modulates intracellular Mtb trafficking and survival

Kuldeep Sachdeva, Manisha Goel, Malvika Sudhakar, Mansi Mehta, Rajmani Raju, Karthik Raman, Amit Singh, Varadharajan Sundaramurthy*,

Journal of Biological Chemistry

295:9192-9210
10.1074/jbc.RA120.012809
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Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis

Karthik Raman, Rohit Vashisht, Nagasuma Chandra,

Molecular BioSystems

5:1740-1751
10.1039/b905817f