About
I am a computational biologist with a Ph.D. in biological sciences from the Academy of Scientific and Innovative Research (AcSIR) at CSIR–Institute of Himalayan Bioresource Technology (CSIR-IHBT), India. My expertise lies in bioinformatics, systems biology, machine learning, and host–pathogen interactions, with a strong background in integrating multi-omics datasets, network biology, and deep learning approaches to uncover molecular mechanisms in plants and microbes.My research interests focus on applying systems and network biology approaches to understand host immune responses, predicting defense-related genes and effector proteins using machine learning, and analyzing high-throughput sequencing data to study plant responses to environmental and pathogenic stresses. I have hands-on experience in developing computational pipelines, designing machine/deep learning algorithms for biological problems, and building bioinformatics tools such as DLNet-HPI (https://gitlab.com/ravisaroch/star-protocol and https://gitlab.com/ravisaroch/dlnet-host-pathogen-interaction) and RicePathDLNet (RicePathDLNet), with ongoing work on EffectorFold for fungal effector prediction. My work has been published in leading journals, including Trends in Plant Science, iScience, and STAR Protocols (Cell Press), and I have contributed to book chapters and computational biology resources.
I have also worked as a project associate and project assistant at CSIR institutes, contributing to projects on high-throughput sequencing, heat stress adaptation, plant–pathogen interactions, and biomarker discovery. Alongside research, I actively engage as a resource person in bioinformatics workshops and training programs, promoting computational approaches in biological sciences. I am deeply motivated to continue advancing computational biology and data-driven discovery, with the goal of contributing to translational research, plant resilience, and innovative solutions in life sciences.
I have also worked as a project associate and project assistant at CSIR institutes, contributing to projects on high-throughput sequencing, heat stress adaptation, plant–pathogen interactions, and biomarker discovery. Alongside research, I actively engage as a resource person in bioinformatics workshops and training programs, promoting computational approaches in biological sciences. I am deeply motivated to continue advancing computational biology and data-driven discovery, with the goal of contributing to translational research, plant resilience, and innovative solutions in life sciences.
- Kumar, R., Acharya, V. (2023) Effector protein structures: a tale of evolutionary relationship. Trends in Plant Science, Cell Press 28:746-748 doi: 10.1016/j.tplants.2023.04.010
- Kumar, R., Khatri, A., Acharya, V. (2022) Deep learning uncovers distinct behaviour of rice network to pathogens' response. iScience, Cell Press 25:104546. doi: 10.1016/j.isci.2022.104546
- Kumar, R., Acharya, V. (2023) Deep learning-based protocol to construct an immune-related gene network of host-pathogen interactions in plants. STAR Protocols, Cell Press 4:101934. doi: 10.1016/j.xpro.2022.101934
[Picture]
Host-Pathogen Interactions Network construction protocol
Talks
- Leveraging machine learning approaches to unravel the plant immune system and enhance effector protein prediction. National Symposium on Molecular Intricacies of Plant-Associated Microorganisms 2025 (MIPAM 2025) at the Indian Institute of Technology, Mandi, India, March 7-8, 2025. MIPAM 2025
- Deep learning architecture for exploring network properties of rice in response to multiple pathogens. 6th Annual Crops in Silico Symposium & Hackathon at the University of Illinois, Urbana-Champaign, USA, May 11-13, 2022 (Virtual) Crops in silico » 2022 Annual Meeting
Posters
- Investigating the host-pathogen interactions through machine learning approaches for enhancing treatment strategies. Kumar, R., & Acharya, V. IPS North Zone Meet and National Symposium of Himalayan Phytopathological Society on "New Vistas in Plant Pathological Research" at Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India, November 7-8, 2024
- Network-based deep learning approach to uncover the plant immune system in response to biotic stresses. Kumar, R., & Acharya, V. 17th Annual International Biocuration Conference at Indian Biological Data Centre (IBDC), Regional Centre for Biotechnology (RCB), Faridabad, India, March 5-8, 2024
Resource Person
- Deep Bioinformatics Boot Camp 2" at CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, and DBT-India, February 18-21, 2025
- Deep Bioinformatics Boot Camp" at CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, and DBT-India, August 28-30, 2023
- Bioinformatics Tools and its Application in Agriculture workshop by CSK Himachal Pradesh Agriculture University, Palampur, Himachal Pradesh, and DBT-India, February 24, 2019
Participation
- Participated in the "NSM HPC Systems& AI: From Theory to Practice" training program at CSIR-Fourth Paradigm Institute (CSIR-4PI), Bengaluru, and C-DAC Bengaluru, Karnataka, India, July 04-05, 2024
- Participated in the Workshop on "Trends in the Evolutionary Systems Biology and Computational Structural Dynamics" at CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, India, March 23-24, 2015